here is the instructions on how to convert your stock 88-91 civic dx dual point harness to a multipoint harness
How To Install...
Multi Point Fuel Injection

Tools
Pick Tools (for depining 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 (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!)
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
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...
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.
Wiring Colors and Functions
DPFI MPFI
Pin # Wire Color Function Wire Color Function
A1 Yellow 2 Aux Injector Brown #1 Injector
A2 Black 1 Main Relay/Ground Black 1 Main Relay/Ground
A3 Yellow 1 Aux Injector Red #2 Injector
A4 Black 2 Main Relay/Ground Black 2 Main Relay/Ground
A5 Red 2 Main Injector Light Blue #3 Injector
A6 Green Purge Cut Off Solenoid Valve (Coil) Green Purge Cut Off Solenoid Valve (Coil)
A7 Red 1 Main Injector Yellow 1 #4 Injector
A8 Yellow 3 Sedan LX A/T
A10 Red EGR Solenoid Control Valve (Coil) (A/T only)
A11 Blue/Yellow EACV (Coil) Blue/Yellow EACV (Coil)
A12 Green/Black 2 Main Relay Green/Black 2 Main Relay
A13 Yellow/Black 2 Main Relay Yellow/Black 2 Main Relay/Injector Resistor Box
A14 Green/Black 1 Main Relay Green/Black 1 Main Relay
A15 Yellow/Black 1 Main Relay Yellow/Black 1 Main Relay/Injector Resistor Box
A16 Brown/Black Ground Brown/Black Ground
A17
A18 Black/Red Ground Black/Red Ground
DPFI MPFI
Pin # Wire Color Function Wire Color Function
B1 White/Green Hazard Fuse White/Green Hazard Fuse
B2 Orange Tandem Control Solenoid Valve Blue 1 Fast Idle Control Solenoid Valve
B3 Yellow A/C Clutch Relay Yellow A/C Clutch Relay
B4 Yellow/Green Radiator Fan Relay Yellow/Green Radiator Fan Relay
B5 White/Yellow Alternator White/Yellow Alternator
B6 Green/Orange Check Engine Warning Light Green/Orange Check Engine Warning Light
B7 Green/Orange A/T Shift Position Console Switch (Park, Neutral)
B8 Blue/Red A/C Switch Blue/Red A/C Switch
B9
B10 Orange Crank Angle Sensor
B11 Green/Black A/T Shift Position Console Switch (Drive)
B12 White Crank Angle Sensor
B13 Blue White Main Relay Blue White Main Relay
B14 Blue 2 To Yellow, To Alternator Blue 2 Alternator
B15 White 1 Ignitor Unit White 1 Ignitor Unit
B16 Yellow/Red Speed Sensor Yellow/Red Speed Sensor
B17 White 2 Ignitor Unit White 2 Ignitor Unit
B18
B19 Green/Red Electric Load Detector Green/Red Electric Load Detector
B20 Brown Ignition Timing Adjusting Connector Brown Ignition Timing Adjusting Connector
DPFI MPFI
Pin # Wire Color Function Wire Color Function
C1 Orange Crank Angle Sensor Blue/Green Cylinder Position Sensor
C2 White 4 Crank Angle Sensor Blue/Yellow Cylinder Position Sensor
C3 Orange/Blue TDC Sensor Orange/Blue TDC Sensor
C4 White/Blue TDC Sensor White/Blue TDC Sensor
C5 Red/Yellow TA Sensor Red/Yellow TA Sensor
C6 Red/White 1 TW Sensor Red/White 1 TW Sensor
C7 Red/Blue Throttle (Position) Angle Sensor (TPS) Red/Blue Throttle (Position) Angle Sensor (TPS)
C8 Yellow EGR Lift Valve Sensor
C9 Red/White 2 PA Sensor Red/White 2 PA Sensor
C10 Green/White 3 Brake Switch Green/White 3 Brake Switch
C11 White 1 MAP Sensor White 1 MAP Sensor
C12 Green/White 2 EGR Lift Valve Sensor/Pa Sensor/Ignition Timing Adjusting Connector/TA Sensor/TPS Sensor/TW Sensor Green White 2 Pa Sensor/Ignition Timing Adjusting Connector/TA Sensor/TPS Sensor/TW Sensor
C13 Yellow/White EGR Lift Valve Sensor/Pa Sensor/TPS Sensor Yellow/White Pa Sensor/TPS Sensor
C14 Green/White 1 MAP Sensor Green/White 1 MAP Sensor
C15 Yellow/Red MAP Sensor Yellow/Red MAP Sensor
C16 White 3 O2 Sensor White 3 O2 Sensor
*All info adapted from the Helms Manual for the 1989 Honda Civic

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


Inside the car at the ECU...
To depin 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 needle (or something thin but strong to pry the pin out of the plug, its a pain in the a s s to do, all I can say is keep trying)...
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 (weird, but trust me on this one).
-Take the pin/wire from B2, depin 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, depin 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 depin them and pull them out.
-Depin 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 (weird, but trust me on this one).
-Take the pin/wire from B2, depin 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, depin 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.