Econoline with newly rebuilt transmission

Hello,
I just had my transmission rebuilt by a local transmission shop, and it is now shifting much better (still not perfect, but it doesn't slam into gear anymore unless I am at full throttle). The problem is that when I really try to get down on it when accelerating, the engine bogs down just after the gear change. The transmission shop updated the pcm, installed new torque converter, rebuilt valve body, did something with a banner kit, and I can't remember what else. I did notice in the engine when it stays at high rpm in second gear (to make a long story short, I limped to the transmission shop in second gear) there is a whistling noise (vacuum maybe). Can a vacuum leak cause this bogging down of the engine? Can it cause the transmission not to shift at the correct points? I have a 351 efi w/ e4od transmission. Thanks for help!!
Micah

Went through a little problem solving flow-chart, and found the catalytic converter to be the problem. Fixed and now works like a dream. I can barely feel my boat behind me. My transmission is now screwing up again. (the thing jumps b/w gears). I can be driving down the road normally and it will just jump to third (or fluxuate b/w 3rd and 4th) and sometimes jump to 1st or 2nd gear. Am taking it back to the shop tomorrow. Hope this helps anyone who suffers from similar problems!

Hey, what happend after you took it back to the tranny shop? Did they solve the problem?

It was the neutral switch on the shifter harness under the drivers seat under vehicle. They ground it to the frame and it shifts great now. They also replaced the computer. It seems they have problems with one of the pins on it which was creating too much resistance causing shifting problems as well (ie not shifting from first gear).