I built an '89 XJ with a D44/D60 combo. Ran 36" IROKS on it. Clearance on the diffs was not an issue but I did shave off about an 1" off the bottom of both diffs. Surprisingly the rear D60 drums and larger D44 calipers worked well with the stock XJ system and could lock up the 36" tires. Specs were, D44 front with 5.38 gears and posi, D60 rear spooled, 36" IROKS, about 9" of lift(custom short arm).
I used the "narrowest" full size D60 I know of, its was from a mid 80s dodge 3/4ton and has a 65" WMS. I paired this up with a front D44, the housing was from a "wide trac" waggy and the knuckles were from a Dodge 3/4ton to match the D60 bolt wheel lug pattern. All Dodge D44s from 1980 thru to 1993 come with flat top knuckles and can be had in either 5 or 8 bolt wheel lug patterns. Also the spring perches on the rear D60 match up almost prefectly to the XJ spring width making it almost bolt right in(have to fab shock mounts).
The D60 is because its CHEAP, parts are EASY to find, and its pretty much bullet proof in a 4.0L powered XJ. My rear D60 is now in its third wheeling rig and all I've ever done is brakes and oil. Its also been spooled since day one. A D60 is about the only axle I would trust to spool since its a "Full Floating" axle. Meaning that NONE of the vehicle weight rests on the axle shafts so you could break one and keep on driving with no problems. Some people even pull the rear shafts if they plan to flat tow the vehicle a long distance.
The D60s biggest draw back is its 8 bolt pattern which means you have to run an 8 bolt pattern on the front and there in no easy way to change this.
My XJ was a great trail rig but I would never daily drive it. In fact I don't think anything over 33s can make a decent daily driver. To get tires that big means big lift and then the steering and control arm angles get all screwed up, plus fuel economy and power go out the window, even if you do regear.
My advice for a daily driver/trail warrior XJ, coming from someone who has built a mild XJ and DD'd it and then built it big;
Get good quality lift kit under 5"
Run 31 or 33s and trim fenders to fit.
Spend the money to get a good quailty steering kit
Selectable lockers front and rear
Stock diffs with chrome moly alloy axls shaft kits and a hub kit fro the d30
An XJ with 33s and selectable lockers and good suspension articulation will go more places than with 35s and poor suspension flex, it will also be easier to build, more reliable and nicer to drive. Think more about how many hours you'll be DDing it on the street vs driving it on the trail.