The shaft was an issue on the earlier 90's with the LT-77's as well, and not all of them got the retrofit parts. I've also heard that in some cases the LT-77's were replaced with R-380's under warranty.
Unfortunately, replacing the shaft means tearing down the transmission. But it is possible that it's already been repaired/upgraded, which is why you need to check before spending money on replacing the whole transmission.
You also mentioned that you need to replace the transfer case, what's wrong with it? They are usually one of the more durable parts of the truck.
My oil line fix
My 100k stopped odometer fix
Brace for impact, I'm in a "modifying mood". Massive thread count inbound.