Looking at the build photos and the track plan the elevated track should not be that close to the last yard switch. After the incline to the upper level it is 3-036 then 1-O36 22.5° and then 1-O36 11.25°. That would change the angle of the whole elevated loop and move the overpass away from those 3 yard switches.
Do you have the 1/4 turn there before the straight?
The other place to look at is in front of the transformer area. There should be a 10"+5"+1 3/4" there before the turn. It looks like the 1 3/4" is missing. That would push/move the upper loop away from the yard switches.
Those are the two places that would change the as built angle/position from the planned angle/position of the elevated loop.
Look where it should be passing over the yard spurs. I see one track joint over the first spur where you would have to slide a trestle a little away from the joint.