1994sn95

Ok guys i just switched my 88gt engine to an 89 engine. It is runnin like crap right now and im still tryin to figure it out. I was wondering if I did something wrong when i took the smog off before i put the motor in.
Here is how i did it:
-took off the pump and ran a shorter belt (84.5)
-cut the egr tube and welded it shut in the two ports at the back of the heads
-blocked off the vacuum lines that go to the smog
-welded the pipe on the exhaust

am i missing something here, and would a problem in the agr somewhere make my car run so rough?
any help is needed. thanks