Hi H.S.Kang,
The schematic of the board is on wiki, here is the link:
http://wiki.analog.com/_media/resources/fpga/xilinx/fmc/fmcomms1-revbschematic.pdf
We also list different configuration options:
http://wiki.analog.com/resources/eval/user-guides/ad-fmcomms1-ebz/hardware/configuration_options
You can bypass the RF, and only come out pf the DAC and get into the ADC. (no VGA)
As far as the clock to ADC and DAC, you have some dividers inside the AD9523-1 you can use to set it.
If you want complete control, you will need replace the 122.88 MHz crystal.
As far as performance of the board with or without RF, I'm sure there are degradation when you are going through the RF but it's not as bad as you might think. It all depends if you are trying to chase the last dB or distortion or SNR,...
I hope this answers your questions,
Charly