This question has been asked before, but the no-pcie and no-pcie-2 branches on github.com/sifive/freedom.git are quite a bit out of sync with the most recent code-base.
While the Freedom U500 on the VC-707 is using the on-board differential clock, the system will not boot w/o the FMC Card providing the PCIe clock.
My goal is to remove the dependency on the FMC module and remove the PCIe interface (or at least disable it).