Details? Did you buy a donor truck? I know the other was electronic shift and used computer feed back. I have an 06 or 07 lol....can't remember. I'd love a manual. It also tows as a primary use.
You asked... (lol).
The 48RE was my only complaint about the truck. Especially when towing. No lockup 'til 3rd gear/30mph was just killing me. Even did a Mystery Switch, but I can see where it'd be easy to do some breakage. Was going to eventually head to Muldoons in NJ and have them rebuild for a towing tranny. In the end, I just couldn't see continuing to live with the 4 speed auto. The shift spread is simply too wide. In hindsight, I am extremely glad I went with the manual. The 48 has a place in sled pulling or racing at a drag strip though.
Been wanting to do the swap for years. Finally got tired of not finding a donor truck (was watching aiia.com & FB) and bought the tranny through M&M out of VA. Good folks to deal with. Cost me commercial market pricing, but gained me a bit of a guarantee. Obviously cost even more due to buying extras elsewhere (nuts/bolts/brackets/shifter/etc). Only 2 pain points in that stuff was the shifter (expensive bugger, even used) and the bracket on the bottom of the tranny. Neither came with the used tranny. Noteworthy that driveshafts had to be shortened/lengthened. Also, the transfer case input shaft has to be changed due to different spline count.
Mechanically, the swap is all like Jeep Legos. From the clutch knockout plate on the firewall to the crossmember holes already in the frame. I got a Stage 2 (stronger pressure plate) single clutch disk from Phoenix Friction in NJ. Using Red Line MTL and one quart of Lucas automatic transmission fixer fluid... I have absolutely zero clutch chatter.
To get the truck running, wiring was actually quite easy. One of the old tranny wires needs to be grounded. I did it "right" by having a clutch switch. Without the clutch safety switch, you might not have cruise control. Two other issues are backup light wiring and the transfer case wiring (I've got the stupid electronic shift). Still working on these two.
I (optionally) did buy EFI Live and gave the computer a lobotomy (reprogrammed the female truck to think it's a male). In reality, there's no benefit (I think) other than to get rid of the PRNDL. The truck doesn't idle or run differently that I can tell. I did think the idle would change. No reason other than my brain thinking about how gas cars change (auto vs manual).
There's a 2" spacer on the back of the motor that does not need to be changed if going to a G56. If you go NV5600, that (and the starter?) need to be swapped.
I would not hesitate to do it again. There are several videos out there that walk through almost everything you need to do.
I've done a few motor/tranny/TC swaps (CJ, Grand Cherokee, J20). The effort is quite comparable.
Other than "Do it", the only advice I'll add is to use a transmission jack and be careful.