Pontiac Sunfire 1997 2.2 runs open loop misfires closed loop

I have been helping my grandson fix his 1997 Pontiac Sunfire 2.2 l. It had overheated and lost a rod bearing. We replaced the short block with a block from a 1999 Chevy Cavalier. Everything sets up correctly and it runs well when it is in open loop. When it changes to closed loop all the parameters that I can see with an OBD II connection (throttle position, oxygen sensor 1, engine temperature) look okay but the engine misfires like crazy and it will not run. Any help greatly appreciated.