Damn this is confusing

Hey my brother has a 94 Honda civic hatch, he put in b16 a2 motor, he
used the air intake manifold from a 94 del sol, Its working but
running like crap. Is there anything he can do/ or should have done to
make it run smoothly? Could it be the wire harness. Bcause it didn't
line up. He has the ecu for both the odb1 and for odb2 doesnt know
which to use? He is using the obd2 now. We already looked online but
none of the converter wires said the would hook to his car. Any info
to where to go from here or web page that might be of some use. Thanks

 

I suggest that you visit this web site:
www.hondatuningmagazine.com

Also, visit a magazine shop and purchase a copy of "Honda Tuning"
magazine. I am a subscriber and have read many articles about switching
engines in Honda cars. In many cases, they explain where they got the
parts needs to make the switch. You may be able to purchase a back issue
where the motor you mentioned is discussed.