1997 Hyundai Elantra the CHECK ENGINE light came on

1997 Hyundai Elantra mileage: 115,000. Ok my Hyundai Elantra was not treated as well as it should have been. I believe the one of the cylinder piston skirts cracked. It was time for a new engine. My mates and I pulled out the old one. Placed in a reconditioned engine. Much better. But. Initially the timing was retarded too far and therefore the engine backfired. I drove about 100 mikes with the engine like this. I got my hands on a timing light and was just about to tune it when the CHECK ENGINE light came on. My manual says that this indicates a problem with the exhaust system. I cannot detect any such problem and the engine appears to be working perfectly (Once I fixed the timing). What do I need to fix? Did the backfiring just fry some environmental circuit? I have heard third hand of an Excel having the same light turn on, nothing wrong with it. Kept on going for years. Any help would be appreciated.