Hot89SI

I am brand new to this site as I inherited this car from my son. Probably doesn't make sense, but the price was right and the SI motor through a rod through the block after my son sucked up a load of water into the intake. Here goes; I put a 94 D15B8 motor into the bay of what was once a D16A6 89 SI. I have the ECU from the 94, but currently running the older 89 ECU. I put the older distributor from the 89 on the newer engine since I didn't have the wiring harness. I am utilizing the intake and header exhaust from the 89 though. The car runs rough and occasionally I get a check engine light (the car actually runs better with it on); gas mileage is down and it won't pass emissions. When you get on it though it seems to pull pretty good and doesn't miss. Do I have to swap heads or is there a conversion for wiring to go to the 94 ECU. Any help would be greatly appreciated; I work on Post at Ft. Lewis and can only get the car registered once I get emissions to pass.