The strength of the driveshaft can be improved, but the space issue really can't be resolved. It's still gotta bridge that gap between transfer case and diff. If you were to upgrade the driveshaft itself, most common procedure would be to get a Slip Yoke Eliminator option along with your new shaft. Logistically, any Jeep with 3 or more inches of lift should go this route. Your Jeep, being an Unlimited, constitutes an exception because it has a longer wheelbase. You'll notice that Dana and even J who is running the exact same lift as you have "hockey pucks" between their center skid and the frame.
This transfer drop kit keeps the angle of the rear shaft from being to great. The steeper the angle, the more prone to vibrations and even breakage. I'd attribute at least one of the blown trasfer cases I've removed to be a result of the lack of a SYE. The angle may not hurt for a while, but eventually putting it through the cycles for a prolonged period of time is too much for the t-case output shaft.
w/o getting all technical, for starters
Longer the DS = Smaller angle
Less angle = Less strain on joints and shaft
Plus with a CV driveshaft there are two U-joints at the junction at the t-case, so the cycle of the DS causes less strain and the angles do not affect it as much.
Length difference between stock and SYE CV DS
You can usually find a SYE kit plus driveshaft deal for about $500
I don't know if this is a necessary option for you right now with your Unlimited DS being longer and your lift just topping off at 3"
Chris has a CV rear driveshaft and thus not hockey pucks, therefore gaining a couple inches of center skid clearance over J and D.
I'd be more inclined to try out one of the skid plates on the market. While not covering the entire DS area, Nth Degree makes a great skid that covers your rear U-joint area all the way back to the diff cover. I noticed you chewed those U-joint strap bolts up a bit too.
