The list is extensive, yet simple.
Work backwards from tire size.
I did a bunch of calculations before I came to the realization that the tire size I wanted would not work with my axles.
From there, choose axles that will fit reasonably close (Scout Dana 44 just a couple of inches off) or prepare for axle width customization.
Don't forget to figure in where the differentials are in relation to the proposed transfer case (L/R/C front and rear).
Get replacement engine measured to make sure it will fit between firewall and radiator, then between hood and proposed axle height. (This is the time to consider if you want A/C and where you can fit a battery too.)
Get replacement transmission/transfer case measured to make sure it will fit to engine (with or without adapters) and the transmission tunnel.
Fab up some engine mounts and modify transmission support.
Suspension? Coil over springs are quite easy to fab and mount while accounting for shock placement.
Get driveshaft lengths measured to find junkyard or order new ones.
The rest was just customizations - upgrade to chrome-moly axles shafts, ARB Lockers, aftermarket gauges, A/C, Tom Woods off-set U-joints, Warn locking hubs, roll bars, front/rear receiver hitches, winch, etc.