Since you have some history & knowledge of the 35, and I have little, you know the score on it, as well as what you require from your Jeep.
If you intend to venture off road more than occasionally, or have winter weather driving to contend with, 4WD is handy. OTOH a 2x4 (moreso with a working limited slip) can do very well.
I feel a Dana 35 Rear is adequate for basic transportation needs and little more. The brakes are smallish, and the housing isn't very sag resistant without trussing. OK to keep one if it works, but not worth dumping much funds and/or time into.
I have no beef with the RR 30s in 99-below XJs. I'd avoid -93 ones with a disconnect axle and I'd install later model (new?) shafts and Spicer 760 UJs. For abuse, I'd truss it and add reinforcement to the control arm mounts.
My latest Jeeps are an 88 XJ Limited and 87 MJ 2x4. Both have D35s... The XJ won't be wheeled much or otherwise abused, so the 35 with Track Loc should prove more than adequate for my use (no abuse...this Jeep has never been off-road that I can tell, and I sort of plan to keep it that way) I will add a LS diff to the front and upgrade to 4.56:1 gears and 30" tires. With the AWD mode 242, it'll be a comfy and capable 'little' Jeep. Any intent of serious work would demand a better rear axle than a 35.
The 2x4 MJ will be getting my other MJ's Metric Ton 44 or a Ford 8.8" Explorer or 9" Lincoln. Limited slip @ 4.10:1, upgraded (alloy) axles and disc brakes whichever case.
I don't have a lot of faith in the Mopar 8.25" simply due to all the vibration issues folks complain about... The 27 spl open diff someone put in my 89 beater was strong enough for 33" with abuse, but for how much longer? I won't know since there is a 30spl MJ 44 in there now. Newer 29 spl 8.25 are stronger, but share the vibe trait. KJ's have added a dampener thingy to the pinion? Band-aid for NVH? These didn't end up on SWB TJs for a reason...
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