Good input...would be tough to lift 3.5" and invest in 39s to simply run trails they could've done in a stock rubi. One could beef up the d44s...what about RCV's and gussets/truss's?Most of the stuff I listed is tied together. If you get 1 ton axles you will need a different tie rod, drag link, and drive shafts than what will work with your stock axles. So if you buy those now and then upgrade axles, you will need to replace all that stuff again. Same with regearing... if you regear your stock axles and then end up replacing them, that's also a waste.
It sounds like you're not really ready to do axles at the moment so personally I would stick with what you have, and take it easy on the trails. Then just triage stuff as it breaks, if it breaks. And like I said before it's entirely possible you will never break anything depending on the type of trails you do, and your driving style. Basically, if you stick to trails that a stock rubicon could do, you should be ok. It's only when you start doing stuff that is a challenge with 37s (or 39s in your case) then you have to watch out.
To give you some sort of reference, I wheeled the hell out of my rig with 37s and stock axles on this trail many times. But the first time I did this tail, I bent an axle flange and chipped 2 ring gear teeth. Just look around and see what kind of rigs are out there on the trail you're doing. If you see full bodied trucks, FJs, TJs on 33s, you should be fine. If all you see is a bunch of buggies on 40s then get ready to break something. Right now you are over-tired and under-axled... so pick your lines based on what your axles can handle, not your tires.
I'd love to hear more about the circumstances surrounding how you broke the teeth and axle flange. Auto or 6 speed?