Ambitious project, but sounds like you know what you're in for. I'd be worried about the head though - if the lump was at 50% and you have compression or leak-down problems you may be in for huge $$$. The S38 head is 2 piece, and if it's not true it needs to be reshaped, not just shaved. The bottom end is pretty well bullet proof, you may not need to hone the cyl walls (they are supposed to be scored, uniformly, by the way). In any case, the parts for the valve train will run you a few shekels.
The Getrag 280 - well, that's just another story
. It may be worth your while to source one that's already rebuilt.
Take lots of pics.