Updating this thread to current day:
The 8.8 swap has been completed, as well as a fuel pump replacement for the sake of preventative maintenance. Having the tank out of the way made the axle swap a much more pleasant experience. I won’t go into detail on the 8.8 swap as it’s well documented elsewhere. I used the Barnes 4wd truss and am a big fan of it, with the only issue being 100% my fault - I welded the shock tabs on backwards. Even after checking.
I needed to relocate the stock spring perches to correct the rear springs bowing after the pinion angle was set for this combo. Instead of relocating the stock perches, I clocked the truss so that the perches sit parallel at ride height, which also pulled the track bar out of the gas tank (they were previously trying to occupy the same space). While at it, the axle got a new pinion seal, outer bearings and seals, Powerstop pads and calipers with the TJ getting new JKS springs and factory bump stops.
Back on the shocks - yes, even after installing the axle to check everything I didn't install the shocks and welded the brackets on backwards. Oops. I torched the old brackets off and welded on a pair of Barnes 4wd curved shock tabs (PN: B4WCSTP). These don’t hang down near as far as the stock units and fixed my issue.
The axle swap and fuel pump install were wrapped up in early November '24 and the Jeep has been chugging along relatively problem free ever since. I do have a P0420 and P0740 code pop up that I need to figure out as the both come back pretty quick after I clear them. I've had 2 instances this summer where the TJ has lost 4th gear, only for it to come right back after it sits overnight both times

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Total miles on the swap: 8,384