Your car is OBD2?? on a 94 civic??
92-95 civics are OBD1, but anyway, you can use an OBD1 or OBD2 harness on the motor and still use the existing harness that is on the car, it doesnt really matter if you use a B-series or D-series harness. But either way you're gonna have to run your VTEC wiring (if you didnt have it previously), knock sensor and wire up the secondaries.