Originally posted by SEEKERone
there are two different versions of OBDII..sometimes called OBDIIa and OBDIIb. 98 and previous civics are OBDIIa..99and after are OBDIIb. if the skiunk2 adapter harness was previously used on the 98 civic that the motor came from, then the harness is for a OBDIIa...if you are now using the 99 harness then you need a OBDIIb aadapter harness. the wiring pinout is very, very different.
<cliff note version> get a new adapter harness for the 99 version
that as your original problem ...as to why it is the way it is now...don't kow.
Haha...this is funny. You can not use the OBD2a engine harness on the OBD2b chassis.
Are you throwing any codes?