Wow.
Okay, there was some correct information in here, but for the most part, I'd rather just list all of the information I can think of pertaining to this topic that I know is true to perhaps help in clarifying some stuff. I know some or all may be redundant, but it'll at least be organized.
- 1992 model year starts wiring\computer language called "OBD1" or On-Board-Diagnostics 1, the first generation. Anything before that is Pre-OBD, or OBD0. OBD1's last year was the model year 1995. 1996-1997 was OBD2a, with 98+ as OBD2b. B is worthless, A is convertible.
- Your 89 CRX Si is MPFI (Multi-Point-Fuel-Injection), OBD0. The engine swap you have is OBD1 MPFI. There is a difference in the wiring between them. The difference is the industry recognized "language" or preset wire routing and plug color\type selection for the harness and connectors.
- In order to use this engine, your best bet is using the 89 CRX Si engine harness. In doing so, you may run your CRX injectors, which will match your injector resistor box. Running the OBD1 injectors will change their type to saturated, not peak-and-hold like the Si's, and will not require the use of the injector resistor box. Eliminating the resistor box from the circuitry is as simple as connecting the wires on either side of it with those that correspond on the opposite side. You would also need the OBD1 injector plugs on your harness. I recommend running the CRX Si injectors, the stock resistor box, and the CRX Si engine harness for this engine. The flow rate between the B18A1 OBD1 injectors and the D16A6 OBD0 injectors remains consistent. It's the impedance, the type (saturated or p-n-h) and the plugs\language they speak that differs. Staying true to the chassis may help ensure ease of the swap, less headaches, more simple trouble-shooting, etc.. It's in your best interest.
- You need to choose which OBD you'd like to run. Zero, or One. Your scenario may be preferable to running the stock Si ECU, which in my experience provides more aggressive results stock for stock with a B18A1, (torque steering like crazy through third and squealing versus a turd-burglar on the PR4 ECU). It will also match your chassis wiring, where as the OBD1 B18A1 ECU will have different connectors, requiring a sometimes costly OBD0-OBD1 ECU Jumper harness, which would be entirely unnecessary for your particular build. If you do not wish to run the stock CRX ECU and want to be sure you have the correct computer, try an OBD0 PR4 LS Ecu, from 90 to 91 only. Also, an OBD1 dizzy coming stock on your motor will require either a jumper harness to convert down to OBD0 if you choose to run that (or you can depin the OBD1 plugs and use OBD0 plugs, the wires are the same color and all, just different plastic holding them), or if you wish, you may use a 90-91 B18A1 distributor with your A6 CRX harness. Depinning is my favorite solution.
- You may also consider running the radiator and fan from the Integra, it's dual core from the factory whereas the CRX is single, and the inlet and outlet pipes correctly match those on the engine, so there is no need for sloppy shims or ghetto rigging to avoid coolant leaks, and you get a factory upgrade on cooling.
- Use 88-89 Integra axles ONLY. EVERYONE on the internet will tell you to run the 90-91 Integra axles which WILL allow the car to run and drive, but will cause future problems with axle binding\premature wear, increased driveline stress\friction\losses, etc... The Civic\CRX 88-91 in America is an ED chassis vehicle, NOT NOT NOT an EF, they were EFs in JAPAN and other countries. They also had optional B-Series motors not just D. In America, the only if not one of the only EF chassis is the 1G Integra (I think only the 88-89, generally, you wouldn't almost ever want 86-87 parts for reference). The outside of the axles fits the CRX splines (DX and Si!), just like the 90-91 LS axles, the insides of the axles that plug into the D-SERIES TRANS of the 88-89 Integra (D16A1, NOT B-series) also happen to plug up into the B-Series intermediate shaft and transmission, just like the 90-91 LS axles do. But the Integra of 90+ housed a B-series like EF's in Japan. So factory, they have a longer axles, by roughly an inch or so of total front chassis\suspension width. So, going down in that width to a ED chassis CRX, which needs the strut tower wall to be banged out for alternator clearance since it's chassis is about 1 inch more narrow, the axles manage to fit, but because they are for a DA chassis integra, the knuckles of the CRX squeeze the CV joints together, reducing the gap in the bearings to the housing. This causes binding under conditions like hard turns. This is why companies who sell remanufactured axles, like Auto-Zone, now sell only brand new axles, because they are cheaper than fixing the THOUSANDS of returned axles every MONTH all across the country from Honda people who choose the wrong swap axles. The 88-89 Integra may be a legit EF chassis like the JDM Civic\CRXs, but it has a D-Series motor factory, not a B, because it's american, which causes the overall chassis\suspension width to match the CRX, making the 88-89 axles the actual CORRECT length to use on a B-Series swapped EF. The only other note of axle mention would be to pry out the dust-rings on the inner side of your knuckles, it's encircles the area where your axles poke through the back of the knuckles, needle nose pliers work great, but WEAR GLOVES. On some cars, this process is a serious knuckle buster!
- As far as the emissions\vacuum nonsense is considered, I'm posting my own thread with questions about my recent B18A swap into my CRX, cause I'm having galloping idle issues and I removed the entire charcoal canister setup, and the purge valves from the firewall and plugged every non-essential vacuum nipple on the manifold. I also, don't have the dash pot on the throttle body, or the bracket of hard vacuum lines on the back of the manifold. The PCV breather box isn't hooked to a PCV valve, the tube just runs straight from one side to the other like it's hardwired. The PCV breather nipple on the valve cover has only a dump tube that goes behind the steering rack. The fuel vapor nipple on the firewall that hooks to the charcoal canister vents to atmosphere. My ECU (PR4 OBD0) reads code 43 and the check engine. Sometimes the CEL isn't on, but the code is still flashing. It's a fuel delivery code of some type, and when it's not galloping at idle, it's idling at 1250, gallops from 1-1500ish under certain coditions, but not always. When I first swapped the motor in, it had no codes and idled at like 5-800 when warm. Now it has the code and idles improperly. Usually, ECU's LEARN their situation after being disconnected from power for a while. I think my learned that it's situation is not proper, which is why it stopped running right without any changes under the hood or to the car at all.
Hope SOMEthing in there helped shed some light on your situation.
Also, there is something you might consider looking at. The idle mixture screw should rarely ever be touched, it's one of the last things you actually use to set your car's idle when it's running PERFECTLY. You may have installed the throttle cable with just a HAIR too little slack. Loosen the nuts on the cable, then by hand tug the cable with even pressure until all of the slack is gone but not moving the throttle plate\butterfly. Then with your other hand, set the rear nut so it holds it right there, without twisting it too much which will cause you to have too little cable length and be holding the plate just a hair open. Once that's set, adjust the other nut, close to the throttle body by TIGHTENING IT with the other nut being held as close to the original position as possible. Test this by flooring the pedal and making sure the plate hits WOT, you check by pressing your finger on the plate to see if it moves any more while someone is flooring the pedal. If it's rock solid, you're getting WOT okay, if the cable has neutral slack off of the pedal and is not holding the plate just slightly more open than normal, you'll have it set correctly for idle too. Your cable may just be a little too tight and causing you to idle a bit higher. The coolant sensor being changed to stock and raising the idle 900 more RPMs is what's probably a key clue here. Use a multimeter and a manual to check your TPS sensor voltage readings, make sure to reset the ECU after each change you make, and ensure your vacuum is well buttoned up and as close to stock as possible, eliminating only the unnecessary stuff and properly capping all unused ports. Go to auto-zone and look for vacuum caps where they sell stuff like oil pan drain plugs and washers, it's usually near there.
If your intake manifold gasket was bad, you'd probably be losing enough coolant to point you right to it. so it's probably not that, but you may try replacing it for benefit of a doubt.
Also, make sure to time your car, with a light, after it's warmed up (fan kicked on twice), and with your ignition advance plug jumpered (it's the yellow boot covering the misc. looking plug on the drivers side of the wiring harness behind the driver's side mount between the strut and headlight wiring. Put a paperclip in it to connect both pins, completing the circuit, and it will stop the ECU from correcting ignition timing on the fly, you have to do this to use a timing light properly, because then the light can show you mechnical timing instead of what the ECU is compensating as it runs.