1997 Chevy Tahoe shifting

1997 Chevy Tahoe, 5.7 liter 4x4 with 123,000 miles, replaced tranny at 66,000 miles. Just replaced the intake manifold gasket which caused service engine soon light to come on. Finally got the p1345 code, my brother who is my mechanic timed it with timing light then realized after the code to line up the distributor with the paint line on the back of the intake. The tranny was shifting a little rough before intake gasket went, got a lot worse when the light was on, runs much smoother now after timing was adjusted correctly but something still isn't right with the tranny. Example-usually happens on the freeway, when you slow down for traffic and then give it gas to speed up or to pass, it shudders, I don't know if it's downshifting or what. Last summer had the full tranny serviced from the Chevy dealer and explained the rough shifting, they checked the u joints and the driveline/shaft to see if there was any play anywhere, they said everything was fine, but something isn't right, just hoping I'm not going for #3 tranny or a rearend work! You guys really seem to know your stuff, any suggestions would be greatly appreciated!