If you are going thru the process of a engine swap why would where the transmission shifter come out at matter? You cut a hole if needed and that is where the shifter sits.
Doing an engine swap isn't plug and play and since you are starting with a 4 cyl engine the Holley swap mounts don't just drop in like they do if you had a 6 cyl.
https://shiftsst.com/1997-2006-jeep-tj
Here is a thread with someone doing a LS swap with the TR4050.
https://wranglertjforum.com/threads/tremec-tr-4050-transmission-swap-kits.24764/#post-960402
Need to do some searching and reading. You do know you'll need a new transfer case or the input gear for your transfer case? A 4 cyl has a 21 spline input gear and you'll need a 23 spline input gear for most transmission you'd want to put behind a LS either manual or automatic.
Try reading some of the build threads on here with engine swaps.
And not that I'm against a GM engine in a Jeep but why a LS swap over a Dodge V-8? Yes I know the LS get better fuel mileage and makes more power easier but I'm just asking? What is your swap budget? Any other mods planned during the engine swap?
Why are you doing the engine swap?