I had a somewhat similar problem at around 35k miles. wouldn't shift from 3rd to 4th , 4th to 5th, etc (and merging into traffic was a safety issue) till i let off the accelarator a bit, and really jerky shifting. I was getting serviced at a dealer back then and they said fuel filter was causing it. It affected fuel pressure (not sure exactly how, fuel pump i guess) and cause the trans to act like it was.
But I have a dsg tranny.
I purchased a 2004 Jetta wagon TDI with automatic/triptronic transmission and 83,000 miles. Had professional 3rd party inspection which found no problems and had it shipped to me. Car arrived with engine light on, no power to climb hills, and major problems in shifting smoothly when just getting going after sitting for a few hours or overnight. Actuator on turbo was bad which was big investment to fix but now it has power when needed. Unfortunately, it is still having trouble shifting from 1st/2nd then 2nd/3rd till car is very very warm. Then it shifts smoothly and has plenty of turbo boost to get up WV hills.
Don't have a local expert close by so I've driven 4 hours each way to Athens, OH to have belts changed/diagnose turbo actuator problem, then to go back once part was in to replace actuator.
So, did the fuel filter address your problem shifting? Do I possibly need a new thermostat so it warms up more quickly? New transmission (I hope not)? Transmission flush (I don't know if that even happens)?
I don't know a lot about cars. I want my car to drive without revving up to 4000 rpms before shifting. I got screwed by a Florida dealership and now am just trying to get this great fuel efficient car to run how it should since the dealership wasn't honest about its problems.
Mariah