That's been my frustration since I built my most recent system last year--manufacturers are vague (or completely silent) on exactly what happens when you use PCIe slots in combinations other than what they think you need. But if you're building a high-end gaming rig, who uses the built-in sound system? And why use the chipset RAID when you can get much better RAID performance with a dual-processor add-in card with a battery-backed cache? (And yes, I would want RAID even with solid state drives for the fault tolerance--drives always fail, even SSDs.)
Thanks for all your input. You've confirmed what I suspected--that I'm dreaming too big.