Interesting setup you have there.
For #3, just to be sure that both the cards are working properly, can you connect monitors (or KVM) to both cards and verify both cards can drive the desktop?
I forget if the CAL samples have a command-line option of choosing the device to run on. But, if you get into programming CAL, you can choose which device to run a kernel on.
The easiest way in Brook+ is via the environment variable BRT_ADAPTER (starting from 0). For each device reported by FindNumDevices, you can open a different shell, set BRT_ADAPTER (to 0,1,...) and run a Brook+ sample.