Can you split the grade? By that I mean in addition the your up grade is there someway you can lower the right of way going under the bridge?
Most folks just look at the rise of an overpass. Depressing the track that will be running under the bridge may also be a way to achieve the desired clearance.
Spliting the incline/decline grade change in the same overall distance of just an incline grade can reduce the rate of grade by half. Or conversely, you can reduce the length of the grade by keeping the percent the same.
Instead of just going up 6 inches over a flat plywood, layout, consider only rising 3" and then cutting a dropped right of way 3" into the framework to split the difference.
If you are using typical 3/4" X 3 1/2" cross members you can use 7" high pieces of plywood as a gusset to add an additional cross member directly below the crossmember needing deeper cutouts.