i have just finished installing a 93 h22a jdm in my 94 accord, i ran into some wiring problems, some of the accords main wiring harness does not fit in the preludes.....on the driver side i was able to fit 2 harness but remains 2 off the motor and 1 on the car that doesnt fit. on the passenger side i was able to fit 2 harness but 2 remains on the car and 1 on the motor that does not fit. It looks like i could cut and extend 1 of the harness from the driver side to the passenger side but not the others.

 

What model of accord is it? Mines a 95 ex and everything fell exactly back into place on the main plugs. If your plugs are not matching up it sounds like you may have used the prelude harnees or there is somethign else wrong.