I have a 05 tl 6spd with 130000 just changed my clutch and flywheel both axles
and steering rack and wheel hub, the mods I've done are pcd rv6 j pipe xlr8 62 solid mounts and lca compliance bushings with h&r drop springs on stock struts.
with all that being done to my car i realize while braking in the clutch is a thud noise every time i take off. i also hear it when i let off the gas and press again.
I don't know whats the problem could it be transmission eternal. I also change my transmission fluid it shift much smoother.please help!!

 

check engine and transmission mounts. Might have missed bolting one down.

 

I didnt use the trans mission mount again, I didnt think it was necessary .

 

So you left the transmission mounts off?

 

yeah the mount on the bottom near the tranny

 

I would go back and look under the car again when you have light. It might not necessarily be hitting things where the mount is, but causing other unintended motor movements.

Put the mount back on and see if that solves your noise problem.