Double check FMC pinout and make sure we are not doing something stupid, like tying one of the many ground pins to power or something
Trace each LVDS signal to each omnetics connector: Polarities right?
Double check pinouts for all ICs
Decoupling caps need to be moved as close a possible to respective ICs. Get rid of power and ground traces wherever possible -- these should dive right into the correct plane.
Make sure high speed lines (1) don't have stubs and (2) stay close if they are differential
Look at ground/power planes in isolation. Make sure there are no long, linear breaks due to closely spaced vias.