I agree with PHIL0426 idea, measure the maximum height of the car from top of rail, remove the existing structural shape, either a I beam or channel, make a taller I beam or channel with the bottom flange and web cut out for clearance, and glue in position on bridge.
You should be able to use Plastruct or Evergreen strip and sheet stock to make this beam, use a styrene cement/glue to make this beam and for attachment to the bridge. This type of modifications are applied to actual structures as clearance requirements change this beam in actual practice would require a structural analysis for stress and welded attachment to the columns. So following this method would add additional interest to the bridge.
One final comment, this method would work for a plastic bridge assembly, I do not know if this Lionel bridge is plastic or metal, if metal you can fabricate a soldered brass beam assembly, your local Hobby Lobby carries K&S Metal brass sheet stock, pricing is okay. This metal can be cut with tin snips and soldered 18 to 20 gauge material would be okay to use in my opinion.
