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Pictures. We need pictures. Your alternator should be mounted with either 2 or three bolts. If you loosen all of them a bit, you'll be able to rotate the alternator around. Rotate it so that it pulls outward, tightening the belt. You may need a helper (i.e. crowbar) for this to get it tight enough. You'll know you have the right tension when you can twist the belt 90 degrees, but no farther.
The shrieking might have been the bearing (smell anything funny?) or it could have been the belt screeching against the pulley.
When you say the crankshaft pulley is half an inch out of alignment, what do you mean by that? Describe it better.
As for the engine vibration, check all of your engine mounts carefully. You could have a broken one, and if you let it go you'll end up with all sorts of engine problems.
The vibration could also be caused by the crankshaft being screwed up - - -start praying that that isn't the case, because if it is, you may as well replace the engine. It'd be cheaper than fixing it, especially since you have the 5SFE. Find someone with a naturally aspirated MR2 that wants a turbo motor - -they'll generally sellt heir 5SFE very cheap.
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