Guys I too am confused as to how you're assembling the diff and trans with problems. The diff is easy to assemble if you follow the instructions.
The only way you could incorrectly assemble the thrust is to not have the race side facing the thrust balls. Even if the washers are different thickness's which I don't believe they are this would not change the overall size of the thrust assembly. The thrust retaining clip should slide right into place as long as the assembly is fully seated.
A standard trick when assembling the diff is to take a pair of pliers and compress the diff spring a few times. This will quicken the break in time and lessen the chance of having a diff that is initially too loose.
Your rear dog bone should be no where near hitting the adjustment screw. If this is the case you've put the diff together wrong. Again make sure you're putting the diff screw in the out drive with the female end. The spring and thrust nut go into the male ended out drive.
The only thing I've seen a few guys miss is the single thin shim between the two inner bearings.
The way I preset my diff is to tighten it fully in small amounts while working the diff a bit. This will prevent any chance of flat spotting the balls. Back it off 1/3 of a turn and use 2 allen wrenches to make sure I can't slip it by hand. Install.
To break it in make 100% sure your slipper is loose! Hold one tire on the ground and work the throttle at low speeds for say 5-10 seconds. Repeat on the other side. Tighten up the slipper and make sure your diff doesn't bark at all.