One option; MTH now makes their bridges "FasTrack Compatible". Sell / replace the bridge you have and use all FasTrack.
Another option is use 027 tinplate. It's a lower profile than the 031. That said, I really don't know if that will correct your alignment issues.
Option #3, put RealTrax on the bridge. MTH has a tinplate transition track too. Connect the FasTrack and RealTrax transition pieces together.