Front & rear axles both out...
The 4.10 D28/35 hybrid on the left, stock D35 3.73 on the right.
Started getting the rear end in place, all went well and got it bolted in place.
Ran into my first problem though, and figured I should document it though in case it helps someone else! So, apparently the Explorer Sport Trac and Explorer rear calipers differ slightly. The Sport Trac calipers are slightly larger overall, and neither sets of my 15" wheels will clear them. While I was having a moment of panic trying to figure out what I can do other than having to buy a set of 16" wheels, my brother did some research and noticed that the Explorer rear calipers looked smaller. So for kicks, we bought one caliper to see if it was smaller and if it would work, and it will. The Explorer caliper bolts onto the Sport Trac caliper bracket.
So if you want to run 15" wheels with an Explorer rear end swap, make sure you get Explorer rear brake calipers and pads if you bought a Sport Trac rear end. The rotors are larger for the Sport Trac, along with the different calipers and pads (compared to the regular Explorer 95-01 rear axle most people use). Otherwise, I believe it's the same basic 8.8 31 spline axle, aside from the brake parts.
Here's a side by side of the Sport Trac (left) vs Explorer rear caliper (right)