3 sizes of 0R (0402, 0603, 0805) could be simplified to use 0603 everywhere?
R33 is the only 49.9Ohm resistor and its value doesn't seem critical. Can it be instead 2x 100Ohm in parallel?
R118 is the only 0201 100Ohm, can it be 0402 instead or Xilinx recommends it to be 0201?
R6 is the only 220Ohm resistor, could be 200Ohm instead
R112, R113 are the only 2k4 resistors, could they be 2k2 or 4k7 (like the rest of IC9 pull-ups)?
R12 is the only 100k resistor, can be replaced by 2x 200k
R152-155 are copied from the System Board where there was one more 4M7 resistor. It's not the case in this design so you can use directly 2x 10M resistors (as specified by CPCI-S) instead of 4x 4M7.