Tools
Pick Tools (for depinning plugs)
Soldering Gun/Iron
Heat Gun (helps a lot for Heatshrinking)
Sewing Needles (for depinning the ECU)
Electrical Tape (for wrapping wires together)
Heat Shrink (for covering and sealing exposed soldered connections)
18AWG Wire

Parts for ZC (D16A8/A9) (supposing you have a complete engine)
Injector Resistor Box (most all Honda ones will work but I recommend getting an Si one)
PM6 Si ECU (good), PG7 Integra ECU (better), or PM7 ZC ECU (BEST!)
Extra ECU pins (only for automatics, or if your intake manifold has an FITV)

Parts for MPFI on DPFI engine
MPFI Manifold (D16A6, Si engine)
MPFI Distributor (D16A6)
Injector Resistor Box (most all Honda ones will work but I recommend getting an Si one)
Injector Plugs (if your Manifold doesn't have them)
PM6 Si ECU
Extra ECU pins (only for automatics, or if your intake manifold has an FITV)

Instructions

What is Multi Point Fuel Injection?
For the 88-91 Honda Civic (and some previous Civics) there were two types of fuel injection. One was Dual Point Fuel Injection (DPFI) which had a system of 2 fuel injectors shooting fuel into a common plenum where the fuel randomly was sucked into whatever cylinder was on the intake stroke at that time. Almost like a glorified carb system. It was good for gas mileage but terrible for performance. The other type of fuel injection was Multi Point Fuel Injection (MPFI). It had 1 dedicated fuel injector for each cylinder (so 4 for a 4 cylinder). This wasn't as good for gas mileage (though far from what I would consider bad) but was much better for performance.

How can I make a DPFI car MPFI?
All it takes to make a DPFI car into MPFI is basically swap around about 6 wires, thats it, not hard at all. MPFI wiring can be done in about 3 hours or less, probably less (especially if your new engine is already MPFI, and you aren't taking any parts off a DPFI engine to make it into MPFI). The main things you do is swap around some wires at the ECU, run some wires into the engine bay, and run a couple wires to a resistor box. Heres how to do it step by step...

Can I do this conversion on an automatic?
Yes, but there are a couple of differences.  You will need an ECU from an automatic car, otherwise your lock-up control solenoid won’t work, and your mileage will suffer.  I would assume your shifter position indicators on your cluster won’t work either.  Also, there is a very slight difference in wiring.  A couple of the wires that are not used by the ECU in a manual are used in an automatic setup.  More on this under Automatics and Exceptions. 

Do it right the first time!
Whenever you do any wiring on your car always solder the wires together and put heatshrink on them for a perfect connection and seal. You will thank yourself in the long run. Also where possible use OEM clips and harnesses from a MPFI car, it will give you a better connection and a cleaner look.

ECU Wiring
The basic idea of wiring for the ECU is you are cutting some wires, adding wires to the ones you cut and running it to the engine bay, or swapping around some wires you cut and attaching them to each other. Here specifically are how they are supposed to be wired. But first here is a diagram of how the ECU pinouts are numbered, the side you are looking at would be the female side (the holes) with the wires coming out of the back of it. If you are still confused by how the pins are number than click here for a picture of the side you are looking at.

*This diagram of the ECU Plugs is taken straight out of the Helm's Manual for the 1989 Honda Civic. Some other MPFI instructions have the plugs a reversed way, or the HASport way. I use the Helms way.

For ZC (D16A8/A9), take a look at this 88 Integra PG7 ECU pin-out.

The ECU is located under the carpet of the passenger footwell...

Automatics and Exceptions
On an automatic car (using an auto ECU), pin B11 is wired to your shifter position switch, D4.  Since you won’t be moving that pin, you will need an extra ECU pin.  If you're using the tried and true "cut" method, put the extra pin in B12.  If you're using the "switch" method, put it in the C2 position.   Other than this, the rest of your conversion should be exactly the same.

Some intake manifolds will have an FITV (fast idle thermo valve/idle up solenoid valve).  If present, it should be located either on the backside of the intake plenum, or under the throttle body. It is up to you whether you want to wire this up or not.  If you choose to, there is a slight difference in wiring.  Pin B2 is wired to the FITV (if present).  Since you won’t be moving that pin to the B10 position, you will need an extra ECU pin and wire to extend into the engine bay.  You will also need a ground for the FITV.  It uses the same ground as the EACV (black/yellow).  Other than this, the rest of your conversion should be exactly the same.

Old vs. New methods
One thing I found out was the following instructions are sort of the old way of doing it. Originally whoever figured all of this out made more work for themselves by having to solder all this stuff he cut up. But if you think about it you can do this a lot easier by following the steps after this one...

Tried and true method
-Pins B10 and B12 are empty meaning there are no wires going into them as a general rule, however some models have a wire at B12 (if you have one that is one there that is one less wire you will need to move).
-Pins B2 and B11 have wires going into them but they are not used for anything on most cars (see Automatics and Exceptions above).
-Take the pin/wire from B2, de-pin it (this means pop it out of the plug) and pin it (pop it into plug) into B10's empty spot, how you have a wire at B10.
-Take the pin/wire from B11, de-pin it and clip it into the B12 spot, now you have a wire at B12.
-Cut the orange C1 wire and white C2 wire "in half" (by cut in half I mean cut the wire making sure to leave enough wire so you can strip and solder them to another wire later). Now when dealing with cutting I will refer to the side of the wire coming from the interior harness as the harness side, and I will refer to the side of the wire coming directly from the ECU's plug (direct ECU connection) as the ECU side (the only plug in question for this step is the ones that go into the ECU).
-At the ECU plug, for C1 and C2 solder and heatshrink wires to them and run them into the engine bay (I did this via the A/C grommets). Mark these wires with a piece of tape saying C1 and C2 on it. Because if you are like me you were using black wire which all looks the same so you need to make sure you know which is which.
-Now connect and solder the ECU side of B10 onto the harness side of the orange C1 wire, then do the same for the ECU side of B12 and the harness side of the white C2 wire.
-Cut wires at A3 and A7, solder and heatshrink wires to the plug side of A3 and A7 and run them into the engine bay, make sure you mark them. Now you should have 4 wires running into your engine bay.

Swap and switch method (less cutting and soldering)
-Pins B10 and B12 are empty meaning there are no wires going into them as a general rule, however some models have a wire at B12. If you have wires there de-pin them and pull them out.
-De-pin C1 and C2 from their plug and plug C1 into B10s spot and C2 into B12s spot. By doing this you just saved yourself the need to solder any cut and solder at least 2 wires.
-Pins B2 and B11 have wires going into them but they are not used for anything on most cars (see Automatics and Exceptions above).
-Take the pin/wire from B2, de-pin it (this means pop it out of the plug). Now solder and heatshrink on a length of wire long enough to reach into the engine bay all the way to about 1ft after the fire wall. I say this because I like to add a plug right after the firewall later on so you can unplug your whole engine harness if you ever need to. You can do this in comfort outside of the car. Once you are done pin this wire into C1's now empty spot.
-Take the pin/wire from B11, de-pin it and solder and heatshrink a length of wire onto it just like you did for B2. Once you are done pin this into C2's now empty spot.
-Cut wires at A3 and A7, solder and heatshrink wires to the plug side of A3 and A7 and run them into the engine bay, make sure you mark them. Now you should have 4 wires running into your engine bay.

Inside the car at the ECU...
To de-pin the wires from the ECU plugs you need to pop out 2 white clips at the top and bottom of the plug, then from the front side you need to use a mini-screwdriver, needle, paperclip, etc.  something strong and thin.  Here is a quick de-pinning how-to.

Your wiring will look something like this...

*I redid my wiring so that I had a plug placed right after the firewall that would allow me to quickly disconnect the Cylinder Position Sensor and 2 of the Fuel Injector wires, good for if you ever have to remove the engine again. The engine harness can now stay right on the car, all you have to do is remove the 2 main plugs and the custom one I added now to remove the engine. There is a tab right under the interior/engine harness plug where another plug can fit. So I added one right there...

I got the plug from the junkyard and just soldered onto the length of wire I cut off.

Engine Wire Harness...
For anyone wondering the answer is no, you cannot simply plug an Si engine harness into a DX car, it just doesn't match up. The easiest way is to modify the DX harness. Also when you swap harnesses you will have 1 white plug left over from a sensor that the DX had that MPFI do not, so don't be concerned.

-If you are swapping the engine and the engine is out of the car then swap the DX harness over to your new engine (Si or ZC). If you are adding MPFI to a DPFI I would try and do this next step with the harness off of the engine.
-Throttle Position Sensor (TPS) wires need to be extended, the TPS is a black sensor on the side of the throttle body, there are 3 wires going to it, extend those, always solder and use heatshrink. On the TPS plug on the DX harness you will see 3 wires going to it, yellow, red, and green, in that order (if you are looking at the top of the clip from left to right on the DX clip). Depin and switch the green and yellow wires around so now the order is green, red, yellow. This is because the DX TPS sensor works in the reverse of the MPFI one, so if you didn't do that your car would think it was at redline when it was suppose to be at idle. So if you have that problem you know you skipped this step.
-Electronic Air Control Valve (EACV) wires need to be extended, the EACV is a rectangular box on the back of the intake manifold, it has 2 wires going to it, solder and heatshrink.

Injectors and Resistor Box...
For OBD-0 MPFI cars they require an Injector Resistor Box. The box transfers the high impedance current the DX has and turns it into the low impedance needed for OBD-0 injectors. Without this box your fuel injectors will get fried. You can use most any Honda Injector Resistor Box. I used to have a 1st Gen Integra one in my car, but its big and ugly and looks like a twinkie. At the junkyard I found a box from an Si so I took that and cut the harness off of it and painted it flat black. The one from the Si looks like a mini stereo amp, looks better and takes up less space than the Integra one.

4G Si Injector Resistor Box...

1G Integra Twinkie looking Injector Resistor Box...

-The DX has 2 injector plugs on it, cut them off as close to the plug as you can. Connect all the yellow/black wires from those injector plug wires and solder them all together. From that combined connection solder on another wire and run it to the yellow/black wire on the Injector Resistor Box.
-Connect the solid yellow wire from the DX injector to the #1 injector (I insert all the signal wires onto the left side of the injector plug, and all the resistor box wires on the right side, though I'm not sure it matters).
-Connect the solid red wire from the DX injector and run it to the #3 injector (onto the left side of the plug, like I mentioned above).
-Connect the A3 wire to the #2 injector (left side).
-Connect the A7 wire to the #4 injector (left side).
-Now run a wire from the right side of each injector plug and connect it to the red/black wires on the injector resistor box (the order doesn't matter from what I've seen).

Cylinder Position Sensor...
The CPS detects when cylinder #1 is at top dead center to help with proper fuel injector timing.

...For DOHC engines such as the ZC

-Connect the C1 wire to the blue/green wire on the Cylinder Position Sensor (a sensor on the exhaust cam of the ZC).
-Connect the C2 wire to the blue/yellow wire on the CPS.

...For SOHC engines such as the Si

-Connect the C1 wire to the blue/green wire on the CPS (the sensor is inside the Distributor on a SOHC engine). For doing this I suggest swapping out to the proper Si distributor plug so it is all plug and play and looks clean.
-Connect the C2 wire to the blue/yellow wire on the CPS.

Also if your engine didn't come with a wire cover try and get one, they make the wiring look a lot cleaner and OEM looking...

Vacuum Hoses
You will see that the Vacuum Hoses for the STD/DX and possibly Si aren't exactly in the same places. But here is how they should be hooked up.

Sensors on the firewall...

The 2 vacuum hoses from the MAP Sensor and Purge Solenoid Valve (PSV) are to be joined together with a "Y" Connector. You should not leave the hose from the PSV vented to the atmosphere because it's job is to open up to release the trapped hydrocarbons inside the charcoal canister into the engine's intake manifold so they can be burned up. If you do not have this system hooked up properly, the hydrocarbons will be released right into the atmosphere which is horrible for the environment. So do your small part and make sure you hook it up correctly.

Notes
When you do this take my word about doing it right the first time. Try and get all the OEM connectors you can get and solder at all connections and heatshrink. When I had my Integra Injector Resistor box with crimped on butt connectors I noticed my car was more sluggish when it was cold than after I installed my Si resistor box with soldered connections and OEM connectors. Also when you do the wiring for the injector plugs make sure you get a pin with a decent length of wiring coming off, then solder on to that, that will ensure you good connection. I originally tried crimping some wire into a pin but you can't solder it because the space in the plug is too small. I ended up having my car running really shitty on 3 cylinders for a long time until I went back and redid it. Another thing is try and use OEM plugs where possible. Get them off of junkyard cars if needed.

Also remember, wire looms are man's best friend. Here is my wiring without looms... MESSY!!!

With wire looms... decently clean...