Yep. It's definitely a leaf spring axle. No wedges to worry about.
Nice that you got a 250 Dana 44 with leaf spring perches instead of the wedges. I guess I should've assumed it was 8 lug from a 3/4 ton because it is paired with a 60 rear. I still
personally feel like a full width 3/4 ton Dana 44 is too wide and heavier than it could be, but you'll be just fine with that. You're going to want to pick up some chromoly shafts. The biggest downside of the 44 is you're limited to a 5-760x sized u-joint, so you'll need to do all you can to support that. RCV's are the best option, but big money. You can also get chromoly u-joints to pair with chromoly shafts, but also big money. Many people have success with just chromoly shafts and OEM Spicer u-joints.
I'm not very knowledge about the Dana 60 rears, but I know they can be hit or miss about the specific combination of parts. You may want to look into it a bit to find out exactly what you have and if its worth running.
I'm looking at shock hoops vs sheet metal shock towers now. Is one inherently stronger that the other? I figure I will probably need them sooner or later. I've found good info on both, but no conclusive comparison. I just want to make sure I do it right the first time, since it's hard to go back from cutting the wheel wells out.
The most common setup I've seen is hoops in the front, towers in the rear. Boostwerks Engineering makes a rear shock tower kit, and its common to use 80's F250 shock towers to graft in. Do a search and you'll find many examples of how people have set things up. I'm actually just getting ready to start doing rear towers on mine.
The front can be a bit trickier.
I've researched myself crazy on the front suspension. I know I will want long arms and probably air shocks or ORIs(probably determined by what isn't backordered 12 mos). But the 3-link vs 4-link debate has me confused. I'm willing to do either one, I just don't know if one is better suited to my needs than the other. Or if one is better suited to the XJ unibody chassis design.
In my opinion, 3 link is better suited for a solid axle that needs to flex significantly. A 4 link with a panhard bar is inherently over constrained and relies on bushing compliance to accommodate the misalignment as the axle flexes. 3 link solves that problem. I see no reason not to go 3 link.
If you're going to coilovers, airshocks, or ORI's, you'll need some serious hoops up front; i.e. tied into the unibody very well and braced across the engine bay and hopefully into a cage as well. Its one thing to put the force of a damper into a hoop/tower, its another to put the spring force into it as well.
The best way you can go about setting up your suspension will be to mock up your axles and tires under the Jeep where you want them with tires
at full bump, then flex your suspension fully to check clearance everywhere. Cut away anything that is interfering until you're happy with the range of travel you're getting. Then, measure for your bump stop heights, shock lengths, driveshaft lengths, brake line lengths, axle vent tube lengths, and limit strap lengths (if you want to use them). With your shock travel lengths you can use the compressed length of the shock to measure up from your axle (at full bump) to find where your upper shock mounts need to be, then build them to be there.