Hey dude, are you still going to go for the manual with a crow cam??? If so, then I would STRONGLY advise against a 3.45...
The crow cam doesn't have all that much up top (without head work), and coupled with a manual box, you're gonna spend your entire life changing gears!!! If I were you, I'd go for a 3.23 at the most (which you might find you've already got).
Otherwise, in answer to your questions:
Yes, the XR6 diff will fit.
Last time I got quotes - ratio change was $400 and rebuild (may be required when getting ratio change) was $450. But this was quite some time ago...
Otherwise, you could spend a liftime hunting at the wreckers.