Things that kill a TR3650:
These are my personal/professional opinions and are based on experience and observations:
#1 Using Royal Purple fluid
This stuff gets good reviews on various forums, but nobody seems to connect the premature failure of their synchro rings to the type of fluid they have been using. When I tear down a TR3650 that has the purple fluid residue the rings are shot and the bearings are pretty much worn as well. the top recommended fluds are 3.0 Liters of Mercon-V or Mobil-1 Multi-Vehicle Synthetic ATF. Ignore filling it to the fill plug. Drain it and install 3.0 Liters (3.2 quarts) of the proper fluid.
#2 Accidentally hitting reverse while aiming for fourth gear while going down the road.
There is no reverse lockout on a TR3650. There is an interlock that won't allow you to shift straight out of fifth into reverse, but you can come across from any other gear at highway speed and hit reverse. This destroys the reverse synchro slider by "laying over" the small engagement teeth on the slider. Often that damaged slider then gets stuck, or becomes hard to get in and out of reverse or fifth gear.
#3 Never checking or changing the fluid in the transmission.
This is particularly bad on the bearings. The fine metal particles in the fluid build up and speed up the wear on the bearings turning everything black inside and coated with a carbon build-up. Besides, if you have a slow leak, you may not run out of fluid since you are refilling it regularly.
#4 Beefing the engine up to over 500 HP and not upgrading to the stronger 26 spline input shaft.
The stock input shafts tend to wring off at about 500 hp on the engine... Once this shaft is upgraded, the next weakest point is third gear.
#5 Installing an aftermarket shfter with improperly adjusted shifter stops.
Aftermarket shifters are great, but there is no need whatsoever for adjustable shifter stops on a TR3650 because the internal stops that are built in the transmission are absolute. Adhustable stops won't hurt anything if they are adjusted right, but if the adjusting nut comes loose, or the adjustment is set wrong, it can keep the transmission from fully engaging a gear. When partially engaged, it will pop out of gear, or damage the synchro.
#6 Ignoring a major vibration at high speeds
Something seems to go wrong with the drive shafts of cars with TR3650 transmissions that make them go way out of balance. This results in a huge vibration. The tail housing is weak on a TR3650 and will eventually crack. In some cases it actually snaps the output shaft. If you get high speed vibrations, get it checked promptly.
#7 Don't put RTV down the bolt holes when reinstalling the shifter
I find lots of the shifter bolt holes to be stripped out. One factor is, of course, that the bolts are easy to start cross-threaded, but people think it will leak if they don't put RTV in the bolt holes. There is even a how-to video from a major aftermarket shifter manufacturer showing to put RTV down the bolt holes. Well, with the cavity full of RTV the bolts tend to strip out the threads in the casting. In one case, I believe the person must have forced them in using an impact wrench. They managed to actually SPLIT OUT the casting material adjacent to three of the four shifter bolts!