Can each transceiver run independently in regards to clock rate?
Yes, each transceiver is fully autonomous. Note that the Tx and Rx side of any given transceiver must operate at the same rate.
For transceivers running at more than 2.5 Gbs, there might be additional restrictions on the number of independent clocks available, because of a limited number of available BREFCLK inputs. For more information on BREFCLK inputs, please see the RocketIO User Guide.
The RocketIO User Guide is available at:
http://www.xilinx.com/support/documentation/virtex-ii_pro_user_guides.htm