Mike,
There are bigger problems with the design. I went over it a bit more thoroughly and found the loops on the left going to the bridge are less than O-72. Initially I had just checked the curves at the top of the loops and they're O-72. I should have remembered that they tighten going to the bridge because I had checked them earlier to make sure they weren't less than O-54.
The other problem is that the upper reversing loop is off kilter because of the cut tracks. They join in SCARM until you disassemble them and try to put them back together or, in this case, try to make changes. The interesting thing is they fit properly using all sectional O-72 tracks and only cutting 1 straight track at the switch, so I'm not sure how you ended up with cut curves and tiny fitters.
At any rate, here's what I've come up with as a possible compromise. The gold, red and green tracks are O-72 and the yellows are O-54. The grade up is 2.9% and down is 3.8%, but should be doable, even if you need to use a yard switcher to push some extra cars up to make a long consist for the Big Boy. BTW, the switch to the grade down is O-72, so the Big Boy can back down and pick up some cars as long as the lead car is past the O-54 switches. The bridge can also be moved up the the NE a bit and the decking adjusted accordingly if needed so the Big Boy can clear the switch and not hit the bridge, but I don't think it'd be a problem either way. You can probably adjust the lower right yellow loop to be more concentric, but I'd add landscaping for some interest and separation.
Oh, and I know you plan to use FlexTrax, but this at least shows how O-54 and O-72 would fit/look. HTH