Rebuild Runs Rough

fluctuation on a fuel injected engine is mostly the problem of a vacuum leak speak lean mixture. check it with a brake cleaner for vacuum leaks. If everything is Ok, i would highly recommend ( in any case ) to to run the EFI in the closed loop mode ( wide band sensor running ) and tune the mixture new, like you bought it new. Every engine needs his own calibrating and you changed a lot of the basic engine! Run a good matching ignition curve matching to your cam, compression ratio and fuel you're using. Good luck.