We just swapped a 2004 5speed 1.8T engine to replace a blown 2002 automatic over the weekend. Oil starvation the head caused the original head to fail (badly). The bottom end of the automatic was in OK shape.
We had to swap the crank shaft from the original auto engine into the manual donor. The shaft was too different in our case. I've read of others modifying an automatic crank to mimic the manual one via grinding, expanding the hole, and placing a new (or other cars) pilot bearing. Going the other direction i.e. placing a manual into an automatic, it isn't possible to do this.
I personally am leery of having the input shaft being slightly off center by just grinding the auto crank nub and altering the pilot bearing hole. Off center is no good at high RPM, even slightly. I cannot comment on the longevity of the components without perfectly centering them. People have done this . . . when placing an automatic donor into a manual care, it does work with altering the crank nub.
To be honest . . . IMO, your best bet is to find a manual donor for a manual car and the same goes for an automatic to an automatic, or if your crankshaft is OK you can swap them.
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