Maybe look at stronger MT's to drop in there. Rule out the NV5600 as it's too slow to shift. In context of stripping gears: The 4L80E isn't that strong and simply isn't a manual trans. (Blown sprag that debris then munched the OD gearset, many ruined TC clutches, and the manual 3rd overrun clutch pack is always the 1st thing I toast.) You will loose MPG with it. The plus side of an auto is being able to keep full power and the turbo wound up during shifts. If you do do the 4L80E get a triple disc converter to fix the OEM weak TCC.
Have you found a way to feed the turbo inlet cold air? It will make a difference out here to compress 120 degree air vs. 200 degree air...
The trans is holding fine with the updated gears. Warwagon the intake stays cool enough. I thought it would suck in hot air but through the scan tool on a hot day it is only 125 deg.