The conversion to std shift is only a bunch of work. The differentials will be different ratio, so you might want to change it too. I would probably change the whole driveshaft as changing only the front half can lead to vibration problems (always mark the two driveshaft sections so they can be installed exactly the same way).
As to the std engine in an automatic; I can tell you that it works. I have done many. I can also tell you that according to the parts it shouldn't work. There are different crankshafts for std trans versus automatic. I am not sure what the differences are but here are two possibilities. First the end of the crank either supports a pilot bearing for clutch cars or the nose of the torque convertor on automatics. I have gone both ways and haven't seen the problem.
The second possible difference is the motor balance. The engine manual used to show how to balance the new flywheel to the old one when being replaced. In other words they weren't individually balanced. If this is the case there ought to be the possibility of great imbalance because of the differences in flywheel weight std vrs auto. Again, I have seen no noticable extra vibration but thats an ambiguous situation with a diesel (bg).
The easiest thing to do would be to install the motor only and see how it works. If there are balance problems it is virtually no extra labor to finish the conversion (compared to what would have been extra to do it in the first place).
Owner 24 bay BSC
Bosch Master, ASE master L1
26 years MB technician