Civics up to 95 - including the CRX - have two separate harnesses, one for the engine that plugs in at the strut towers, and one for the ECU to the dash.
96-00 D-Series Civic's use a one piece engine harness to the ECU. It connects to the dash harness by way of a green plug near the ECU plugs, and a plug on the driver's side strut tower. The wires in these plugs do not coincide with the wires in the CRX's strut tower plugs.
This is the complete OBD2 engine harness. No cuts or splices are made to it. The metal bracket and rubber bushing where it passes through the firewall should be removed. Any other brackets and holders should be removed as well.
Due to inaccurate and vague documentation, I decided to go to the junkyard and rip out a dash harness from a manual trans EK. To get it out, I had to cut it in half unfortunately. Many wire color/stripe combinations are repeated, but to match them up from one side of the cut to the other, I noted the silver dots. There are several green/black wires for instance, but one will have one silver dot repeated about every inch, another will have two.
Finding what plug near the fusebox the wire terminates at still doesn't tell you much. From there I used my roommate's HX as a reference. The wires that had me guessing turned out to be for the fuel tank pressure sensor and air conditioning. Some wires are marked online as "Auto trans" which is completely false, most notably the backup light switch.
There's a grey rectangular case securing all the wires underneath the pedals. You cut the tape and then pry it open carefully not to damage it to the point it wont snap back together.
In order to have unrestricted access I deemed it prudent to pull the cotter pin and just let the gas pedal dangle. A lot of times, pulling more parts out than necessary is faster than leaving it together and working around it.
I left the split loom that goes over the center tunnel intact since it's easy to pull a wire on one side and see it move on the other.
At this point the wiring splits in different directions with some of it going out to the driver's side strut tower plug, some heading toward the main relay, and some going to the gauge cluster. That covers all the wires we care about at least.
THIS IS WHAT HELD THIS PROJECT UP FOR AN ENTIRE WINTER. Inside the blue tape is an oem main relay splice found on DPFI cars only, and not documented anywhere. This little splice causes a neat problem where the engine continues running with the key removed! Especially fun when gasoline is shooting everywhere due to a hose clamp on the fpr being overlooked! Oh, and here's a hint: the engine doesn't stall when you disconnect the battery!
On DPFI cars, the fuel injectors and fuel pump are both on the latched side of the main relay. You have to cut this connection and separate them so that the ECU can deactivate the main relay at will. Main relays on MPFI cars are wired the same as EK's and every other 90's Honda I looked at (Accord, Integra, Prelude, etc).
Here is the driver's strut tower plug. Originally I thought that I would adapt it to the OBD2 harness's strut tower plug to it, but as it turns out, none of the wires apply. Most of the wires were removed. Some were repurposed.
I got a female driver's strut tower plug from the junkyard to make it easy to probe wires.
As you can see in the finished product, the original strut tower harness isn't involved at all. The dash side of the OBD2 harness came from the junkyard. I cut the wires as long as I could reasonably get to. Running these wires through the firewall cleanly was difficult.
These are the CRX's passenger side strut tower plugs unplugged and removed from the brackets. The bracket isn't reused.
I pulled the split loom off to separate out a couple wires that had to be snipped so that the harness could go through the firewall.
After cutting a couple wires to the fuse box and removing the split loom, the CRX passenger side strut tower harness was pulled through the firewall for dissection. Then the OBD2 harness was ran through the firewall, along with some wires reconnecting to the fusebox (ECU power and ELD). I slid split loom over the wires to keep them secure, but held off on the electrical tape until the project was completed.
As I confirmed each wire, I temporarily connected it, tested it at the ECU or cluster, then soldered and heat shrank it. Some wires were labeled on each end to be reused rather than running a new wire from the ECU all the way out of the firewall.
This is the original CRX ECU harness, hacked up for a [crummy] MPFI conversion. Some extra wires were run to an OBD1 conversion harness that was connected to a chipped p28. These plug connectors would be removed from the car, but I kept them intact until the last moment so that I could more easily identify what the wires were for. All of the OBD0 pinouts I found online had errors, so every wire was verified by hand.
At this point I was probing every wire, and in many cases, literally pulling wires out of the split loom and physically following them to their conclusion. In blue there's an OBD2 jumper harness that I could strip and hook up test connections without ever violating the OBD2 engine harness. In the end it went back to my toolbox to be abused while troubleshooting other cars.
Everything was coming together here. You can see that the two-pin service check connector is wired up, as well as the OBD2 diagnostic port. Once the engine was running, it was useful to hook up a scanner and see if any sensors still needed to be hooked up.
This is the finished product, all wires connected and secured. The original ECU harness plugs are completely gone, as well as each of the original strut tower plugs. Unused wires were completely removed from the harness.
The CRX is now effectively OBD2. Any OBD2 engine could be dropped in and plugged up. It's not easily reversible - to convert back to OBD0 you'd have to get another dash harness.
OBD2 diagnostics are fully functional, and you can jumper the SCS to set the ignition timing or manually read the trouble codes.
Here you can see the black harness bracket and the blue connector. I scavenged these off junkyard EKs to use to secure the engine harness so it doesn't rub under vibration. On EKs, the perfect bracket is down near the battery tray right where the harness comes out of the firewall, held on by a 10mm bolt.
These plugs are left unused. Just ziptie them up and hide them. This is the power steering pressure sensor plug, the electric speed sensor plug, and a plug for the charcoal canister purge valve.