I have a 04 A4 quattro manual six speed. when ever i accelerate the engine seems to judder at about 2800 rpm. my check engine light came on then went back out if i stay in the gas when this happens. seems to only happen in 4-6th gear. what would cause this?

 

Are you putting only premium fuel? Have you tried checking the codes? You might need a new coil pack here and there.

 

Coil packs often cause issues like this and can be unpredicatable. Often only shuddering under any load (accelerating and up hills), but ok when cruising.
There is a known issue with coil packs in the early models. You might even be able to get them fixed through a recall in the US. Have a look around