What? NO!
EK and EG harness are nowhere NEAR identical...They aren't compatible. Period.
The sensors plugs are mostly the same, and in the same location for the most part, that's about it. Injector plugs are different, the distributor plug is different, the EK has a CKF sensor whilst the EG doesn't, the EG has the IAT on the intake manifold whilst the EK has it on the intake tract...
That, and the harnesses themselves are DIFFERENT. On an EG, the engine harness connects to the in-car harness at each shock tower. The EK connects to the driver's side of the in-car harness on the driver's side shock tower, but the EK's engine harness goes directly to the ECU on the passenger side - there isn't any type of plug or connector between the engine harness and the in-car harness on the passenger side shock tower (like in the EG). The only connection to the in-car harness that the EK has is a small plug inside of the vehicle that connects the engine harness to the dash harness.
If you want to use an EK engine harness in your EG, you are going to have to re-wire your ENTIRE car. That means pulling all your interior, pulling your dash, finding a complete harness from an EK, and putting the ENTIRE EK harness in.
If you want to use an OBD2 ecu, you're pretty much going to have to just add wires to your existing harness (such as for the CKF and secondary 02)...it's going to be time consuming, but NOWHERE near as time consuming as trying to convert the whole thing to an EK harness.
If they're giving you problems about the jumper, just go wire-by-wire where the OBD1 ecu plugs plug into the jumper, and bypass the plugs (meaning clip the wire on either side of the plugs and solder them together), so that you have your EG harness soldered to the jumper, and the jumper plugged into your ecu. Again, it's going to be time-consuming, but NOWHERE near as time consuming as swapping out your ENTIRE engine, dash, and in-car harnesses.
edit: Also, if your car is a 92, he shouldn't be trying to pull OBD2 codes from it...You might want to just try going to a different ref before anything else. Just because he frowns on something doesn't make it illegal. He could 'frown on' yellow cars if he wanted to, but that doesn't mean that he can fail them simply because they're yellow.