Be careful! You don't want to get 1/2 through a build and have the wife loose her mind over what you have spent, then you have to bail on it. I am a firm believer in full disclosure to the better half.
These rigs are not the kind of rigs folks want "Numbers matching" or totally "factory correct". Generally speaking, the ones I see sell for the most are the ones that are totally driveable, minor mods here and there (maybe up to a 4" lift, upgraded radio, sound deadener, etc.), everything works (A/C, cruise, etc.), and a modern engine or 401. You see a lot of LS swaps and a few Hemi swaps. If you build your 360, build it so you can drive it every day. Put a better cam (but not crazy), intake, headers, etc. then top it with EFI. If you have deeper pockets, put in an LS or Hemi and a 4 speed auto. FSJs, in my opinion, are not good rigs to build for value. Build it to enjoy it.
The trans you have now is bulletproof if set up/rebuilt correctly. The transfer case is OK'ish. You will probably want to convert it to part time (with a mile marker kit) if it's not already. Parts for that case are getting hard to find (AMHIK). You may want to just bite the bullet and change trans/case. An AW4 is a good trans to swap in because it bolts to your 360. Then you get a good transfer case with it. You will probably need to swap your front axle to a driver's drop but that is not a big deal.
Here are some great builds (in my opinion) that you should catch up on.