gmbellino: I took my car to the dealer today to see if their 'master' tech could diagnose the clunk in my car. They diagnosed it as not a click, but a groan which appears to be coming from the front sway bar bushings. I think they have no idea what they were looking for on my car, but maybe this is a place to start with the noise you are experiencing. There is no way my click is bushing related as it goes away once there is some temperature in the driveline (maybe 100degF+). Have a look at your swaybar endlink bushings.
spec2speed: I did manage to replace my transmission fluid with Amsoil GL-4 and it had no effect on the noise. I have also developed a leak coming from the shift rod/tail shaft (under the airbox where the shifter cables attach to the transmission). The leak is bad enough that I have a drip on the garage floor developing. Can you inspect your transmission for a leak in this area?
The reason I took the car to the dealer is a suspicion that the click is related to the leak. Possibly the click is the shaft moving out of position, allowing the seal to open up. But still doesn't make sense that the noise goes away with increased temperature. The fluid has its highest viscosity when cold, so I'd assume that the noise would get worse with increased temperature, but is not the case.
I had my co-worker drive my car home today from the dealership to see what he thought. And he seemed to think it was coming from the rear, and an obvious click and not a groan as the dealership mis-diagnosed.
As I've driven the car the last few weeks, the click is still there when the e-brake is pulled (which disconnects the rear diff). So there is always negative torque being applied to the rear axle with the e-brake on and the click still is there seemingly coming from the front (transmission, transfer case, axles, driveshaft, etc.). Don't think it can be any sort of motor mount or rubber bushing. Still wondering if the leak and click are related. If you get a chance, try pulling the e-brake up a click or two while driving the car when cold and apply throttle in 1st or 2nd gear, going on-and-off load. Don't push in the clutch or shift gears when doing this test. Let me know if you still think the crunch/click is coming from the rear.
The dealership wants $30 for the seal and $700 to install. Makes sense as I'm sure it takes a full day to pull the transmission, pull apart, replace seal, and re-install. I'm capable of performing the seal replacement, just need to get a hold of a service manual. Maybe if I have the transmission apart I can check for wear and clearances to make sure the click isn't coming from the transmission.
In the end I paid $102 for a car wash at the dealer today. Going to call the service director tomorrow to see if he has any ideas.