How Bizarre

I have an S4 with 100k miles on it. I just had a new RS4 clutch and stock flywheel installed at a local shop. When I got the car back, I noticed that it shook a little at idle, and then made all sorts of noises and vibrated over 3000 rpm. I felt like it was an exhaust leak, but when I took it back to the shop, they said it was the motor mounts. The clutch and shifter seem to be working well, so I don't think they messed up on the installation of the clutch and flywheel. Over 3000 rpm, the car shakes and the engine noise is way louder than it used to be. Also, I can hear a whining sound that I think is from the turbo(s) when they spool up and down. Power seems to be normal. When I'm cruising at any speed, the noise and vibration isn't too bad, it's primarily when I'm on the gas. Could this be the motor mounts? I know they leaked out all of their purple fluid. The shop said they would charge me about $2300 for parts and labor to do the motor mounts. I had to pass on that. Could they have messed up the clutch and flywheel installation and that is what's causing the issues? Thanks for any comments.