Did you replace the driveshaft yourself, or have it done? With it disconnected from the rear, slide the yoke all the way into the trans, then pull it back an inch. That's about where it wants to be when all is connected, with the wheels on the ground (suspension loaded). Raising the body of the car (lowering the axle) will pull the slip yoke out some. Whereas lowering the body with lowering springs, if you have done that, will drive the yoke in further. If your yoke is bottoming out, the driveshaft would need to be shortened.

 

Did it myself, with just the rear lifted -- suspension *not* loaded. I did slide it all the way into the trans, but I don't believe the rear connection comes forward at all -- yet, I don't think I pulled on it to test. In that case, there really isn't any adjustment when installing the shaft, it has to be where it mates to the rear connection. What am I missing here?

My cars are not lowered.

 

For all you know, the noise you hear might not even be related to the driveshaft. If you want to monitor it, you could make a magic marker stripe on the slip yoke and see how much forward movement you get by where the seal wears off the mark. Do you still have the old driveshaft? You can compare the shiny spot on that yoke to the one you have now to see if it's in deeper. Or take accurate center-to-center u-joint measurements and compare the two.