'Yotas are tough, no question. And they're very reliable and look like a lot of fun to build.
However, I'm an XJ man.
XJs aren't too expensive to lift if you cut to the chase and do it the right way. Only way to go is with Rubicon Express; yes its a little more expensive, but its worth every penny cause RE is exclusive to Jeep suspensions.
XJ drivetrains are somewhat weak unfortunately. The front HP Dana 30 was equipped with weak 260x joints and was a vacuum disco up till '91 I believe. The D30 was then loaded with the stronger 297x D44 shafts and joints, which remedeed the vac-disco. I think in '00, the HP housing on the D30 was replaced by the standard cut D30 housing, but still have the D44 shafts and 297x joints (HP housings are around 20%-30% stronger though). The rear D35c is the main weak link here, with weak ass 27 splined shafts and flimsy tubes. In '91, the 35c was replaced by the Chrysler 8.25, however, these also feature C-clips and 27 spline shafts, but the ring gear is larger than the 35c as well as the tubes. However, in '97, the stronger version of the 8.25 came out featuring 29 splined shafts which are almost comparable to D44 strength. I've got quite a few buddies running locked and geared 35s on the newer 8.25s. If you're a little skeptical on the stock axles, find an '87-'91 Wagoneer and snag its D44s. They're just a tad wider, but are nearly bolt up, but need bracket mods first. I will be swapping in Waggies sometime before Spring hopefully.
Also, if you look hard enough, a factory D44 rear w/ 30 splined shafts can be had out of either an '87 or '88 XJ w/ the tow package. These are the golden nuggets of XJs and are kinda hard to find. Superior Axle and Gear now makes a Super44 kit that comes with an Ox or ARB and 33 splined shafts for the XJ D44.
Most common ratios for XJs are 3.07s and 3.55s, I think 3.73s can also be found, but are more common in TJs. Also, YJ 4 bangers sometimes came stock with 4.10s or 4.11s.
XJ t-cases are pretty stout from the factory but have ****ty slip yokes on the rear outputs. These can be handled with an SYE (slip yoke eliminator) which converts the slip yoke to a fixed yoke allowing you to run bigger lifts with virtually no vibes from the transfercase, but you'll need to invest in a pricey CV rear driveshaft. XJs came with the part-time NP-231 transfercase and the full time NP-242. I'm not sure of the 242 ratio, but the 231 features a 2.72:1 stock, which is pretty descent. Also, RE offers a "hack and tap" SYE which requires some cutting, grinding and tapping to the stock yoke, but its only $200, the '97 XJ SYEs are only $100. A lot of guys are running the RE hack and tap SYE and using stock XJ front driveshafts in the rear. This proves to be a fairly stout combo and I have yet to see failure.
The only XJ tranny that I'm familiar with is the AW4 auto. I think they also run the AX-15 manual and a few others, but I really don't have any experience with these or even know if that is correct, so don't quote me. The AW4 is a good solid auto with overdrive. If all possible, get the 4.0L straight 6 engine, you won't regret it. Its very reliable and PLENTY strong for the weight of the XJ.
Thats about as much as I can think of. Really, if you decide to go with the XJ, you won't be let down, they kick ass on the trail. Enough room for your gear and when built right, can more than hang with the SWB guys. If you go with the XJ, you need to decide on the size of tire you wanna run and what your budget is.
Hope this helps man, cause that took me forever to type.