The problem is not on the separation.
The problen is when you try and stick the transmission back into the engine.
You need to be very careful when you slide the transmission input shaft into the pilot bearing / rear eccentric shaft hole.
If you don't align the two and try and force things to go in, you're most likely to damage one or more of the delicate needle bearings in the pilot bearing itself.
Once you damage one of these needle bearings, they will break and pop out.
Once that happens, the little needle bearing pieces will cause the transmission input shaft to intermittently sieze inside the rear eccentric shaft hole.
This does two things:
1) This causes the vehicle to creep even though your foot is down on the clutch pedal, because the engine and the rest of the drivetrain are intermittently sized together, and
2) This causes problems trying to shift gears, as the engine and rest of the drivetrain cannot be properly disengaged so that the vehicle speed is not matched with the engine speed (via normal use of the transmission synchronizers).
This problem and it's headaches will get worse and worse until all of a sudden, the problem will disappear like magic.
This is why all of the needle bearings have broken and fallen out and cannot interfere as described above.
-Ted
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