Wow, that's a lot of parts changing.
With the MT, the persistent sense of the clutch slipping is often caused by an axle that either has a bad/broken CV joint (even though it's not hanging down), or is slightly out of the side of the differential.
When that happens, the ability of the engine to propel the car depends solely on the AWD viscous coupler inside the MT center differential. The coupler is not likely to provide the full torque capacity that a regular MT clutch has, and can "slip". In some cases, if the viscous coupler has failed totally (e.g., if the seals on the coupler have allowed the viscous fluid to leak out) and no longer works, it could leave a MT unable to move.
Raise the car and check each axle to see if the shafts on either side of each joint can be turned independently of the other (they shouldn't). Also, check that the inner end of the axles are fully inserted into the differential, locked in place, and unable to be pulled out except with force, e.g., a lever. If they have a baffle plate on the inner end (originals do), the baffle should appear to be unusually close to the differential case. If the axle moves out only a quarter inch or so, it disconnects from the side gear inside the differential and propulsion there is lost.
There's a fair number of threads and posts involving ATs and MTs with bad axles and axles or have pulled out. Given what has already been done, I think this might be something to verify before any other parts are replaced.