Clean way
This method requires removing your factory harness and removing all the tape and loom. When you do this, make sure all plugs are marked and use some tape, wire tire, something, to still keep the wires kind of grouped together to prevent a big mess. Usually I just remove the looming and just wrap some tape around it once to keep it together.
Once you have the factory harness out, you can either go ahead and take all the loom out, be sure to mark where the factory mounting places are if you want to keep those, or you can just do it as you go. Either way you will end up with most of the harness un-loomed.
After that, go to your donor harness and remove the tape and loom from it, but don't worry about taping it up to keep it grouped.Here you need to remove all 4 injector clips and wires, the resistor box plug, and the distributor plug with the Blue/Green and Blue/Yellow wires intact.
To Depin the wires from the plug, simply look at the pin side of the plug, you will see a small tab by the pins, insert a small flathead, pick or paper clip and press the pin back and pull the wire out of the other side.
Have your Factory harness laid out on the floor, ground or table some where. We will take care of the easy plug first.
Distributor Wiring
Find your OE Square Distributor plug. Take one wire out at a time and move it over to your new Round plug, matching the colors to the distributor side of the plug. You will notice there are 2 White wires, don't worry, if you look closely you will see one is not grouped with another wire like the rest. It is this way on both plugs, so just match those 2 up.
After you get done with that, you will be left with an empty square plug which you can toss, and a new round plug with 2 new wires you need to run. Simply run them along the harness with the rest of the wires up to the main plug on the strut tower.
You can now pin them into your new 4 wire connector(can be bought from local electronics store, maybe hardware store, or local salvage yard). I love using older Honda plugs because they are easy to de-pin and move where you need to without having to cut and solder wires.
Now to the fuel injectors:
Go find your Primary and Seconday Fuel Injector plugs on your factory harness. Your Primary Injector is a Brown plug with a Red and Yellow/Black wire, your Secondary Injector is a Green plug with a Yellow and Yellow/black wire. Remove both of these from the harness, but do not de-pin them yet, just lay them to the side. Now keep in mind where they were coming out of the factory loom because you will want to run your new injectors out of there.
Now that those 2 are out of the way(for the most part). Lay down your new injector plugs and run your #1 Injector wire and #3 Injector wires to the same plug your factory injectors were in. Also run all the Red/Black wires to this side. Your #1 Injector wire will be brown wire, while the #3 will be a light blue wire.
Now depin your factory Secondary Injector's Yellow wire and replace it with your new #1 Brown wire. Next replace the factory Primary Injector's Red wire with your new #3 Light Blue wire.
Now to get power to your resistor box. See the Yellow/Black wire on the green plug? Its going to the main engine harness plug, same that your injectors are at. Now depin the Yellow/Black wire for your Primary Injector and replace it with the Yellow/Black wire coming from your Resistor box plug. Simply toss your factory injector clip and wires off in the trash or wherever, your done with it. But you still have your Secondary Injector hanging on by one wire, just cut the wire and heat shrink the end of it. You won't be replacing that with anything, but you don't want to have an open hole on the plug, so we will just leave the wire there and heat shrink it so it doesn't come in contact with anything.
This takes care of that side of it, but you still have 2 Injectors to wire in. You will be left with a Red wire for your #2 Injector and a Yellow wire for your #4 Injector. Even though you just removed this color wires from your stock harness, they do not go to that side. Run these 2 wires along your harness, taping as needed along the way, and over to the Right side strut tower where your 2 new distributor wires are. Add these to your plug over here.
One last modification to your engine harness and you should be set. Find your Throttle Position Sensor(TPS) and swap your outside 2 wires on it. If you forget to do this when you start your car, even with you not having your foot on the gas, it will think its at WOT, and as you apply pressure to the peddle it will think pressure is being released. You may want to move where this sensor comes out of the harness to where the ground wires are at the thermostat.
At this point you can wrap everything back up, loom it up, tape it up, all that fun stuff. If its possible, you can go ahead and put the harness back in and mock it up before you tape it up to make sure you have taken care of everything. This step is a little easier when everything is out of the car, but possible with it in the car. If you need to, mock your new intake manifold up with a couple nuts holding it on to make sure everything reaches and is put back where it belongs.
Installing the Manifold
Once you are happy with where everything is running and you have your new harness wrapped up. Go ahead and install it in the car for the final time. Now follow your Haynes/Chilton manual and install your new Intake Manifold. Be sure to use a new gasket.
Also go ahead and install your new MPFI Distributor. If you haven't removed the DPFI Distributor yet, make a mark along the tab on the distributor and the mounting tab on the head. Go ahead and remove the 3 bolts holding the distributor to the head. Before you unplug your plug wires, make a note of your firing order(1-3-4-2). Now remove your DPFI Distributor. You won't be able to transfer that mark you made on it to your new distributor perfectly, but you can get close. You can hold the tabs end to end to transfer the mark over, but I doubt it will be perfect. After you have your mark on there, go ahead and install it into the head and put the bolts back in snug. Line up your marks the best you can and finish tightening the bolts. Install your plug wires back on, its the same firing order as before.
After you have that done, make sure everything is plugged back where it belongs and your almost done under the hood.
ECU
Now under the hood, everything should be back to normal, except you now have a MPFI manifold on and a new 4 wire plug on the right tower.
Now take the other part of that plug and run you 4 wires out of it. If its not possible to keep the same color wires, simply make a note of the new colors and where they went to somewhere. Give yourself plenty of wire to run to the passenger foot well and give you some room to work with. Tape everything up, atleast enough to get your through the firewall and run your new wires through the firewall.
There are a couple options here: You can drill a new hole and insert a grommet on it to keep the metal off the wires, or you can make a small slit in the current rubber boot the harness is coming through and insert your wires through it. Its a little tricky on the other side either way you go because of the dash and all the components behind it, so if you choose to drill, make sure you check the other side before you drill.
Once you have the wires inside, finish pulling them through and then go back to the engine bay and finish up your wires under here. You can tape them to the current harness, or simply zip tie them. Its easier to do this after you get the wires inside because it gives you more room to work with to get them through the firewall. After you have them tied up, your done under your hood other than re-connecting your battery, unless your battery isn't under the hood, then you can close your hood.
Now to the ECU. If you haven't already, pull your carpet back and you will see a nice shiny plate there with a little hole. Remove the 4 nuts holding this down and remove it, now you have access to your ECU. You will notice there are 3 plugs going into the ECU. The first plug will have 15 spots for wires(one in the middle is empty), this one is referred to as Plug A. Your second plug will have 20 spots, this is Plug B. And your last one has 16 spots and is Plug C. Plug A is a White plug, while the other 2 are Black.
Remove all the plugs and remove the ECU. First thing you will want to do is move the wires in C1 and C2. The numbers will run with Odds on the top side of the harness(the side with the clip that holds the plug in) and Evens on the bottom. #1 being the Top Left wire looking at the backside of the plug(the wire side)
It is possible to de-pin these, but they are a little trickier and either require a really small screwdriver, paper clip, or the specail tool. It has been awhile since I did mine, so please someone help me out on this one.
If you can't de-pin them or don't feel like messing with it, cut the wire a couple inches back, still leave enough to work with on both sides. You will be moving the wire at C1 to B10, and C2 will go to B12. If your cutting wires, you can cut these back how ever far you want, you won't be needing the wires coming from B10 or B12 again. Once those 2 are moved, you can now wire in your 2 new distributor wires.
If you cut wires, just solder these into the old wires. If you depined them, cut the ends off the wires that were in B10 and B12 and solder these onto the end of your new wires. Now insert your Blue/Green wire into C1, and your Blue/Yellow wire will go into C2. The distributor wiring is done.
For that last little bit: now you will mess with Plug A. You need to run your #2 Injector wire to A3, and your #4 Injector Wire to A7. The current wires in these spots will be the same as the wires originally in Plug B. They won't be needed anymore, so you can simply cut them and reuse their ends.
After all that is done, plug up your PM6 ECU, reconnect the battery and start her up. Now you should have a MPFI intake while still retaining a stock looking harness.