Whenever you need extra clearance for an overpass you can depress the bottom track by removing the Homasote and taper the track down, go under the over pass and taper back up..
If you need even more clearance use a saber saw and cut out the decking along each side of the lower track and push the grade down under and back up again.
Other things to do is to use a girder bridge for the upper track with only thin metal plate directly under the ties. No plywood or road bed at the actual short span overpass.
Several other ways to reduce the rate of climb. I go nutz reducing grades. Got the most recent grade down to +/- 1%
