The HDx board should go into slot 2+3 of the G5, and the FC card in slot 4 (the one that is farthest away from the graphics card). What FC card do you use? Do you use the latest drivers for the FC card?
If you still have performance problems on your XServe RAID, try
downgrading its firmware to 1.32/1.26, which is included in this updater, I think. When we upgraded the RAID firmware to 1.5 we had all kind of performance problems that were fixed by downgrading to 1.32/1.26 again.