Well my 98 is starting to worry me with a lack of repair/upgrade funds shadowing over my head. I started getting a clunk sound from the rear when I put the vehicle in reverse or first and let out the clutch. I put it on a hoist and turned the driveshaft with no slop in in the U-joints, but I couldnt tell if the noise was from the trans or the rear. Im starting to think its pinion wear, but I feel like Im getting a one track mind, can anyone help me out?

 

I had a similar problem to what you are talking about. My car has the 4R70W trans and it sounded like yours is doing the same thing that mine is. That leads me to believe that your problem is in the rearend, not the trans. It might be that the pinion gears or the gears on the bearings on the pinion gear shaft are worn down. It could also mean that the preload on the pinion gear was not done right if you've had aftermarket gears installed. Get under your car if you can and see if you can push up on the rear of the driveshaft, just in front of the yoke. If your driveshaft moves AT ALL, I mean even a millimeter, then something is wrong. Your driveshaft should not move at all. If you have had any work done in your rearend lately, I would take it back to the place that did the work. I hope this helps

 

My 98 Cobra had a similar clunk that turned out to be an upper rear control arm...

 

Yeah, upper control arm it sounds like, same problem in my car.