does the check engine light stay or go away? do you know how to pull the check engine code on that one or is it possible? Did you do the swap yourself or did you have someone who does swaps do it? Cause it sounds like it is having problems on the startup which can be attributed to those wires you are talking about. I thought if it both were obd1 everything would stay the same......also, maybe the harness for those wires on your civic are located somewhere else different than the integra and you need to get a harness that will reach to that place....