Sorry you're having trouble. Here are my thoughts:
(1) Put a 4" spirit level across the wye switch from left to right. If the train is leaning downhill to its left at all, that might cause this problem.
(2) Is there any chance that the wood strips you added between the rails to make your grade crossing are pinching the rearmost flanged wheels, which in turn limits the ability of the front drivers to follow the curve?
(3) Does this loco have a tether, infrared wiring, or any kind of special drawbar that prevents the rear of the loco from swiveling as needed?
(4) Last thought re: gauging, etc.: All 3-rail locos have side to side play in the axles, so that they can negotiate sharp curves. But that's limited somewhat by one-piece side rods. (I've found that on MTH locomotives especially, there is so little play in the drive rods, they prefer curves one size larger than they are rated for on the box.) Despite only having six driving wheels, these Moguls have a LONG wheelbase. When your loco is on the problem switch, is there any slack in the connecting rods, or are they bound tight?
I think these locos have a "bottom plate" retaining the wheels and axles. So if the front wheelset is out of gauge you remove it from the loco to regauge it. Heck, you can (and probably should) order a replacement wheelset from Lionel. It might be gauged correctly, and it's probably good to get a spare while parts are available.
My $.02. Good luck and if you solve it, please post back with the solution!