I recently bought a Audi A4 1.8t 1999.5 (manual)and have noticed that the car stutters when I am accelerating out of second gear. It usually happens around 2500-3000 rpm. The gear is fully engaged but it feels like it slips for a very quick split second and then regains its composure. Has anyone else felt this? I dont' think it's turbo lag because it has power, then slips, and then regains it again. It isn't very noticable, I'm just very picky.

For me at least it is associated with having the AC on. Try turning the AC off I bet your hestitation is gone. Have you chipped yet, this can make it even more pronounced.