I have that too. I've heard this is fairly common on Z cars. If I'm careful to get a smooth up shift its fine but the least hard clutch release causes the thump. It never does it on down shifts. Mine will also make that horrible noise if I let the engine get too low in RPMs and it starts to lug, sounds like the whole rear end is falling apart. Some say get a solid diff mount to fix it, some say that will transfer a lot of noise. I know there is some play, probably too much in the rear driveshaft U-joint too, that will be fixed when I do the LT1 swap.