LOVE these old Chiefs... been trying to find one since I sold my scout a few months ago.
If you decide to go fuel injection and dont want to shell out the $$$ for a Howell kit. Check Binderplanet for the GM TBI conversion they wrote up for IH 345's. It'll work just the same on a 360. The guy who wrote it goes by Bill USN-1 I believe. Probably the most thorough explanation of the conversion on the web as long as you dont mind doing some junkyard searching for the TBI, computer, and a few other things.
On the transfer case...the 727 when well maintained is a pretty solid transmission and you can rebuild it in your garage over a weekend. (There are videos of the complete teardown and rebuild on Youtube).
I'd personally be inclined to go to a center drop TCase like a Dana 300 behind a 727 and just find a centered rear Dana 44 from a different FSJ. Just my $0.02
Time to start searching the texas craigslists for Cherokees...