the problem here is you have a car that is OBDII.a with a motor that is OBDII.b. Here is what i did to get mine to work (i have almost the same deal you do) i got a 96 EX harness (which obviously you have) plugged that into the b16a2 (you have to extend a few wires). i then got a P28 ecu (92-95 OBDI civic ex ecu) programmed to run a DOHC vtec motor. then got a conversion harness (got it off
www.thepartstrader.com, there are many people who make their own and sell them, much cheaper this way, and they work the same.) this way i could plug the P28 ecu into the 96EX harness. this way is very clean, and no cut wires. if you try to use the SI harness, you run into problems because of the 2 different OBDII versions. hope this helps.. oh, if you use a reprogrammed P28, it usually disables the knock sensor and 2nd O2 sensor, so no need to wire those up.