When I had my engine out, I went ahead and replaced the clutch. I put in an RPS six puck. Now when I push in the clutch in first gear, there is a hard clunk. It only does this at mid to high rpm's, and only in first gear. Anyone have any idea what this could be?

Give me boost or give me death!

The clunk is metal to metal contact. I will have to think about this one for a moment.

RPS clutches WILL break! Look for stress fractures on the clutch hub. Many MK3 owners have had issues. I don't know if this is the reason for your clunk, but it is relevant all the same.

Charcoal 1990 Turbo 5-speed
48k mile engine installed 10/13/03. 8k on 1.2mm HKS MHG and ARP studs, engine, turbo, and trans from Genotti Performance in Warrington, MO. Thanks Robert! Installed: RT Downpipe, Test pipe, Blitz NUR Spec, Bosch BOV, K&N FIPK, Electric Fan, JBLMK3 PVC intercooler piping, Cusco catch can mod,...more to come.

After driving it a little more, I noticed it seemed to be coming from the rear. The thump occures in the first couple gears. If I let my foot off the gas first, and then push in the clutch, it doesn't really do it. Also, when I shift to either forth or fifth, and I don't match the revs perfectly, there is a really violent shaking from the rear as I let out the clutch and the rpm's come back up. It feels like the splin in the u-joint is slipping or something. Does this sound like a bad u-joint?

Give me boost or give me death!

that sounds plausible.

Also, check the center bearing of the driveshaft (yeah, we have one, sux!)

If its toast, it takes about an hour to a couple of hours to repair. You can also go with a one piece aluminum driveshaft and solve that problem.

yeah, id definately go with a one piece driveshaft. I dont think it will give you any monsterous gains, but it should make things a bit smoother.