Recently read that the plan for the Howard Street Tunnel was roof notching and removal of roadbed as much as possible and then rebuilding track with metal ties to lower the track height. Don't know if this is something that would work here.
Here is another idea:
This picture is of a "Y" tie used in Germany. It has a low profile and is supposedly very stable. I was not aware of this product.
Y-shaped ties - An unusual form of tie is the Y-shaped tie, first developed in 1983. Compared to conventional ties the volume of ballast required is reduced due to the load-spreading characteristics of the Y-tie. Noise levels are high but the resistance to track movement is very good.
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