Something has been over looked that's for sure. If it ran fine before you took it apart and now it does not its something that was done incorrect. Running rough suggests timing marks aren't right or its missing for some reason like crank sensor got hit or something. Check compression, verify a thing or two... Take it back apart inspect all the marks its easy to be a tooth off. Make sure everythings right,, if you have balance shafts check all those marks. Mistakes are made sometimes, odds are its a easy fix you just have to get dirty again.