cadillac trouble shoot

i have a 1990 cadillac deville fwd.i replaced the engine about a month ago,i put a 4.9 that came out of a 1993 deville.the original engine was a 4.5 litter.im having problems,the engine is running a little rough.i checked the fuel preassure and its under 40.i replaced the fuel pump about a year ago,i replaced the fuel filter last week.what else should i check for.