Haven't really been active with the truck in years... Long story short... life happened, busy with a bunch of other things, yada yada yada. Anyways, I still have the truck and decided to start working on it again. Still runs and drives great but I have always wanted a 5 speed with a manual transfer case so here we are. I saw a trans from a 98 4.0 with 95k on it pop up and was able to talk down the price a good amount. I have had a manual transfer case from a 2003 level 2 laying around for years so it was time to put that to use. I kept the automatic harness and computer with the shift indicator pulled off the auto trans and put into neutral. Onto the parts list:

98 4.0 manual trans with 95k (came with part of the wiring harness so I was able to take the reverse light pig tail from it). Replaced input and output shaft seals and installed a new reverse light switch.
03 BW1354 manual transfer case
Hurst trans shifter (modified with notch in base plate for venting and a custom paper gasket)
FX4 Level 2 manual transfer case shift arm and new linkage from NOS
FX4 Level 2 shift boots and bezel. Took me years to find a bezel lol
FX4 Level 2 floor plate
FX4 Level 2 shift *****
New manual flywheel and flex plate (reused the auto crankshaft bolts)
ACDelco manual starter
New rear main seal
Pedal assembly from a 99
Luk clutch kit, slave cylinder, and master
New rear driveshaft flange on the transfer case side to make the 03 t-case bolt to my driveshaft with a 1330x1310 u-joint.

I believe that is it... Will edit this post if I left anything out. Onto the pics:

Misc. Parts shot on the bench:



Shifter arms, *****, and bezel:



Shipped the trans to my construction job site to use the forklift for unload and avoid additional freight charges:



Trans with shifters on it:



Tail housing pulled for output shaft seal replacement:



Tail housing back on with new reverse light switch:



Truck in the garage ready for the tear down:



Exhaust out... the bolts on the manifolds were the worst part of the whole swap. Only broke 1 out of 4 though:



Driveshafts, cross member, electric shift transfer case, and trans cooler lines all disconnected so I could pull the bell housing bolts and drop the trans:



Old electric shift transfer case:



Auto 5R55E out:



While I did the swap I also did the water pump, thermostat, thermostat housing, and valve cover gaskets. Cleaned up the valve covers real good and painted them old ford blue:



Hurst shifter mods:





Trans tunnel with auto components:



Broken exhaust bolt out. Retapped the holes in the manifolds and installed all new bolts:



Rear main, manual flex plate, pilot bearing, and flywheel installed (surface rust on flywheel from sitting for so long):



Clutch and pressure plate installed:



Turns out Luk slave cylinders are FTE:



Carpet pulled back for floor plate install:



Interior stripped of auto components minus the steering column shroud. I have a manual one ready to install now:



Manual trans installed:



Shifters installed:







Reverse lights wired into auto harness:



Clutch pedal all set up with master cylinder and slave bled:



1330x1310 adapter for the transfer case output flange (I removed the rust from the t-case flange prior to install of the driveshaft):



Test drive video:



All in all, the truck drives great. Clutch is nice firm as well; the master was prefilled but I did a gravity bleed for 3 reservoirs of fluid and then did a vacuum bleed for a while just to be sure. Very happy with the feel of the manual! Big thanks to @Fordzilla80 , he was incredibly helpful during this whole thing. Feel free to ask any questions