Vibration/ idle problem

I have a 04 b6 3.0 with the tip tronic trans car has 65k on it now. Last week was at a light when the car just started vibrating, I can feel it in the seats and even the exhaust note sounds a bit off, but it only does it in drive or reverse...not in park or neutral. So I figured I might have bad trans mounts, I had one that was totally gone and the other looked fine, but I changed them both.
That didn't fix the problem, I looked at the snub mount it visually looked good, mechanic said motor mounts were fine as well.The car recently started idling funny when I shift in or out of park the idle will surge about 200-300rpm between normal rpm for about maybe 1 minute then return to normal car also recently just started feeling like once in awhile it doesn't want to accelerate right, like it drags azz falls into limp mode then goes back to normal? and it started shifting hard into drive from park.
A2gtinut vag comed the car to reset my headlamps and check for any faults,,,,there were none I was thinking maybe trans controller,but vag showed no faults with it. car is 100 percent stockany ideas?