I had a problem with the tranny shifting rough, it shifts smooth again. The only things I did was:
-Replaced 3 vacuum hoses,
These 2:

Going to This Box(nope havent looked the part up yet):

And replaced this Hose as well:
-Adjusted the TPS with a filler gauge and Ohm meter by the toyota manual pdf.
Now it shifts smooth just like it came from the factory.
Not sure which one of these things did the trick because the TPS was pretty much on the money anyways when i checked it's previous position.
So possibly one of these vacuum hoses had a leak causing havok on the tranny for some reason.
If anyone has a clue why this worked?