Still the same answer as above from Grant.....shifter, T-case, wiring harnesses, ECUs and who knows what else
The Limiteds have the VF4BM transfer case with Torsen differential that has an electric shift transfer with and ECU that controls it and a solid pass side front axle.
The TE'S have the VF2A part time transfer case with a mechanical shifter and an electric actuator(ADD) that locks front axles.It's manual shifter moves the forks that change the gears and a switch sends a signal to actuate an electric motor on the front axle that basically takes the place of manually locking in the hubs of many moons ago.
The SR5's as of 2013 have the VF2A with both the electric transfer shifter and the electric ADD front axle connector.
If it's reliability your worried about ,the VF4BM and it's electric actuator has been out over 10 years in hundreds of thousands of Toyota,Lexus and Land Cruiser vehicles and has proven to be very reliable. Now the seals on the shifter to transfer housing went bad in some of the older ones and leaked oil and the transfer case has to be torn down to change them which makes it a big job if done right.Supposed different/better seals were incorporated years ago and mine shifts instantly,smooth as butter and is dry as a bone. From what I've read,not many have failed to shift and leave you possibly stuck/stranded as in can't lock it into 4x4 on the trail.With your full time your always in 4x4 anyways in all 3 shift positions and your ARB lockers can be activated in all 3 too making it VERY reliable.
It's been discussed before and you can search on your own for ADD actuator problems on part time FJ's and they can and have left people without 4x4 as the electric actuator contacts are housed down on the front axle where it's vulnerable to mud,water, salt ect.
I wouldn't even know why or where to start to retrofit a manual shifter to a VF4BM transfer case but I'm sure somebody would switch(pun intended) you your full time for part time system and that would be the cheapest, easiest way if you REALLY need the manual shifter.:noidea: