..... You could take a rzeppa and run it like you want, the true cv will cancel out the vibes from the single ujoint on the pinion. Unfortunately, only the stocker uses this. AEV is still working on theirs and Jim Reel is in collaboration with RCV. If not, you may develop certain vibrations than can cause damage to your entire drivetrain.
You can currently send your front driveshaft to AEV for their rebuilding to a thinner profile which eleminates the boot tearing (and so eventual front DS death) on skids, exhaust cross over or auto tranny pan.
Another alternative is to replace the JKU's skids with DS freindly skids, River Raiders Off Road and others offer skids with plenty of clearence.
As far as pinion angles, using AEV's front control arm relocation brackets helps limit drive line vertical movement when the front end flexes and so pinion angle changes, either droop or stuff. Moreover, and counter to any other control arm set up, pinion angle is reduced on droop by repositioning the mounting points of the upper and lower control arms relative to each other.
For the rear, not pushing the axle back with longer lower control arms without compensating with longer upper control arms should keep a rear DS happy, at least on a JKU.
I've got 19,500 miles on my oem front and rear DS with no issues with AEV's 4.5" suspension.
As I wrote earlier, if drivabilty is an important goal, then go 5.13's. Returning to "stock" final drive ratio might be ok, but you've got the extra weight and the trailer to consider as well. The weight's there 24-7-365, but the trailer is there ?. If you're pulling the trailer a lot, then I would go 5.13's for sure, but the drivablity would be my goal over milage. Saving some $'s on fuel at the expense of constantly struggling up the highway would rain on my days of adventure/fun/freedom to get the heck out of Dodge City.
BTW, a change in milage of 1mpg and assuming 20k miles/year results in increased or decreased fuel use of 114gals/year.
JPK