Just an FYI, the 99+ axle shafts are actually quite a bit beefier than on the TrackKicks except where they taper down to the same size at the splines. Attached is a great picture from the parts catalogue that illustrates this.
I'm in the same boat, I plan on wheeling my Tracker harder and harder in the future but it will be a few years before that happens so I have lots of time to consider my options. It seems some people have been fine with 31's and lockers while others have had problems, so I think I will take my chances and just make sure that I don't abuse it too much. The options I am considering for the rear:
Option 1: Ford 9 inch. Takes care of everything, don't have to worry about strength, lockers or gears. But doing an axles swap seems scary, and I would definately need another DD before then so I can leave it on jackstands for a couple weeks (or more).
Option 2: Replace side gears and axles shafts. Since the axle tubes are bigger there has been some speculation that you can replace the sidegears and use D44 (size & splined) axles shafts. Several of ARB's carrier's have interchangeable sidegears, so you could swap the small suzuki 26 spline sidegears for D44 sidegears. Yankeetim was looking into this, but I think the custom axle shafts were going to be EXPEN$$$$IVE. If you could find a place to make them at a reasonable price this seems like it could be a weekend project: pull the axle shafts, pull the 3rd, replace sidegears and put it back together.