So about 2 years ago I was at this same point with the question to stroke the 4.0 6cyl or find an LSx pull out to drop in. I really like in-line 6's from my Toyota Supra's of past, Jeep 4.0 and Cummins. I ended up doing a low compression stroker build to my 4.0 complete with Hesco aluminum head and all the fancy internals so I could Turbo charge the 4.6 into a reliable 450hp/450lb beast of an in-line 6. Problem popped up with the lack of ECU tuning with the 91 YJ and pretty sure a piston or two may have suffered fuel washed eating up a piston or two on the interstate 2 weeks back. So now I'm back to square one and bought a LS2 complete take out w/55k miles out of a 2007 TrailblazerSS last week because it was going to cost almost as much to rebuild the bottom end of my 4.6 stroker and still have tuning issues.

The current rig:
1991 Jeep YJ w/40" tires, D60 rear, D60HP front w/Drivers Drop, NV3550, AtlasII 3.8, 3" body life and spring over axle on 4" lift leaf springs IIRC

I plan to go with a NV4500 as I just like having total control over the power output and keeping heat and voodoo magic at a minimum. With already having a 3" body lift I'm hoping not to have to modify the trans hump as the interior is LineX'd and have fancy carpet kit and center console. My only other concern with NV4500 is the 2" longer then the NV3550 but my hope is that with the LS2 and electric fans that I'm running I should be able to shove the LS2 forward at least an inch if not two. I have stretched the front end forward 6" which moved gear box and axle forward 6" too. If I have to shorten rear drive shaft any more I'll end up having to upgrade to a High Pinion rear sooner then I had planned and still hesitant to go High Pinion in the rear.

So far these are my other plans:

Novak Engine Mounts (MORE isn't making one for LS yet and AdvAdapters cradle is way too cumbersome)

LS2 upgrades
Texas Speed 224R/114LSR Cam
Trust intake
Headers ???? going to need some sort of block hugger and Novak seems as good as any.
Clutch? Still not sure about this, like a Centerforce setup but I'll also need a flywheel and it starts getting really pricey!

I'll send off stock harness and ecu to be modified and mapped accordingly for simple install, any solid recommendations appreciated.

Speedo I'm ok with as the AtlasII already sends my speedo the necessary signal to stock gauge and no auto ECU to fool with.