I gotta de clunk too. When letting out the clutch at idle w/ no throttle I can hear the thud, sounded like play in the drivetrain. I could also hear a rattling noise coming from the rear end when going over bumps. I took it to a tranny shop and we put the car on a lift-we could grab the rear wheels and turn it with our hands back and forth about 3" clunk to clunk. we could also grab the driveshaft and wiggle it back and forth about 3" clunk to clunk-way too much play. We pulled off the plate over the gears and found out that the pinion bearing was shot. I have heard that this commonly goes out on late model GT's, I guess its true. Nitrous and hard driving probably didnt help either (I did have redline sythetic oil too). They are now pricing a new pinion bearing assembly which stock on a 00 gt is a 27 spline. The part is $300, labor $300. My mechanic is also going to check out options for a beefier assembly, although going with a 31 spline we will have to change the axles too. I'm hoping that some sort of aftermarket 27 spline pinion will work so I won't have to change the axles. If I go back with the factory pinion set I might as well set an appointment now to have it yanked again in about 8k miles! My car only has 11k on it now. I'm smugly glad that I didnt even bother with trying a warranty repair-screw Ford service I cant even get them to answer the phone. Id rather pay a fellow enthusiast who will let me stand in his bay and watch the repairs! I am in Austin and am using Dyer's on Lamar. The owner has an SS that runs 11's all motor-he gave me a fun ride back to my office this morning-try getting that at Lief Johnson Ford! They would have pulled it apart and denied the warranty repair and stuck me with a much larger bill.
Anyway, I bet you have the same problem. My shifting is notchier than hell too, we are hoping a cable adjustment will help that. Otherwise-well I'd rather not think about it!
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Black 2000 GT,5 spd,17" wheels,4:10's, HPM Megabite Jr LCA's, Flowmasters, Steeda pulleys, timing adjuster (11 deg), K&N filter, Nitrous Express w/purge (75shot currently),NGK spark plugs (lower heat range than stock plugs), airbox silencer removed
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