You didn't mention what tire size you plan on running, I'm still curious there...
And fair enough - I like messing around with things for nothing else but the sake of messing with things. That said, on a rig that I wheel and would wheel hard enough to warrant such meticulous work, I certainly wouldn't run such a bastardized setup with everything requiring custom parts (like your rear axle shafts for example).
The biggest Dana 44 axle tubes that I know of are the 76-79 HP versions, which come with 3" x 1/2" tube. Every D60KP axle I've ever worked on has a 3.125" x 1/2" tube. Not sure how you're going to make that work but even still, I see no point in spending the time (even with free parts) as GM flattop knuckles and any of the aftermarket versions are plenty strong and have been wheeled heavily on 37" tires with full-sized (read "heavier"!) rigs without much issue. You can gain all of the advantages of losing the axle bearings and getting manual hubs simply by retaining the Dana 44 stuff. You also get notably better brakes that are more easily adapted to work with the TJ's booster and master size. I'm not sure where you're getting bigger u-joints from, as all late model Dana 44's utilize the 297x joint (same as the factory TJ). The Jana 54 kit can be tedious but I have heard nothing but good things and Carl is a good guy.
For the rear axle, I still do not see what advantage the work brings to you. The factory 14B brakes won't work with your factory brake setup without a lot of work. You can of course run aftermarket JB6 or El Dorado calipers but they really offer no advantage in braking over the factory discs, and then you still have to make the e-brakes work with the factory setup. There is no denying the strength of FF 14B axle shafts, but unless you're upgrading the 8.8's carrier to something bigger, you'll never notice the advantage of a full float conversion, particularly in a <4000 lb rig. I believe this is why all the "full foat conversions" of the 90's era died off soon after being released (but perhaps I'm missing something).
Seems like you're trying best to balance clearance and strength, while getting some width (but not necessarily full width). I'm having a hard time seeing how your setup would be advantageous more so than a comparably built D44HP/F8.8 from a full-size Bronco or similar. I mean hell if you already have a D60KP and 14B FF around, you might as well go big or go home - you can easily narrow a Dana 60 to Dana 44 full-size width (65-67" depending) and can use wheels with more BS to bring it even narrower together. You can then shave the 14B as much as you can and run the appropriate hubs/wheel combo to get a width you want.
I have always wanted to narrow a D60HP/60HD combo to ~65.5" (with a 64.5" Dodge rear) and run that with a stretched SWB rig. I was headed that direction with my YJ at the time but ended up getting my old TJ which I ended up liking a lot (A/C is nice in Arizona lol). I still think that a somewhat narrow rig on 37-38" tires with a 101-103" WB would work very well in AZ trails. Now that I'm back in the east coast, I'd be more inclined to just run a set of SD axles full width and go with high BS wheels.