A Toyota parts rep. priced the auto-TT swap at just over $10K. That's assuming buying all brand new parts through him (he's got the best prices by far on Toyota parts). The tranny itself is $6K, so buying a used tranny (~$2500-$3K) saves a few grand, as well as getting used driveshafts, and whatever else you can get your hands on. This price was for doing a very complete and thorough swap, so I'm pretty sure it included the rear end, as well as a clutch. That misc. bullshit adds up, though.

As far as rear ends go, I THINK the auto rears are the same on NA and TT cars, which are fairly stout, and should be enough for decent power levels, however the ratios are surely different.