The "AWW" 5-speed gearbox used in the 1989-1991 manual transmission V8 models does hold up to the torque of the 3.6 engine pretty well, as it was reinforced (stronger gear wheels, wider synchronizing disks). So, if you have a factory 5-speed where just the engine was swapped - no need to do anything.
If your car is an aftermarket "auto-to-manual" conversion that utilizes a gearbox from the Type44 quattro (AOA, ADZ...) however, then you should indeed be careful about applying all that torque, as these transmissions are not really up tp the task of handling the torque of the 4.2 engine in the long run. It'll most problably be fine for a daily driver, but I`d refrain from using such a setup on the strip or at stoplight races...
Just bear in mind that there`s more to swap than the transmission itself, if you want to convert to a 6-speed. You'd need a driveshaft from a 6-speed model, rework the shift linkage and the mounting brackets (both requires custom welding) and use a wild mix from 5-and 6-speed sourced parts for flywheel and clutch.
6-speed V8s were never sold in the US - the manual trans models were dropped for 1992.
The transmissions from the 1992-1996 "C4" S4/S6 are mechanically identical to the CBM/CBN one used in the 1992-1994 euro-only manual V8s. You could use any of these instead (in fact, any transmission of the C** family would be useable, including the CBR from the RS2 that is the strongest of the lot).
