Hesitation in 3rd and 4th (please help!)

[HoodStrype]

Hey guys... after about 5 or 6 minutes of driving I hit the gas or downshift to 3rd and give the car gas and it hesitates really bad. Bad enough to take it back home! This seems to be a low rpm problem, but when you drive normally in 4th (and 5th) it becomes a bad problem as well.
I put a 1" spacer (clearance problems) on saturday and that's when the problem started. We also connected some vacuum lines that were out of whack and I'm fairly sure we got it right. We thought it had a huge cam until we fixed some vacuum problems . I am wondering if it is the TPS because it now surges a little (throttle at 1000) and we took it off w/o adjusting it when we reconnected it. So if anyone has an idea I'm very appreciative! I think I'm at a loss until I can change or set the TPS at 099. But if that doesn't work... Thanks!