Well, it all worked after a couple weeks of reading. The only thing left is a SAS expander later. Any recommendations?

Biostar TA890FXE
AMD Phenom II Black 3.2ghz
16gb G.Skill Sniper DDR3 1600 (PC3 12800)
3ware 9690SA-4i
3ware Battery Backup Unit
4x Samsung Spinpoint F3 1tb hard drives (3ware SATA RAID5)
2x Samsung Spinpoint F3 1tb hard drives (AHCI, onboard SATA)
Norco RPC-4220 Case
Antec Earthwatts 750 PSU
6x Masscool fans (replaced Norco's noisy Delta fans)
Lite-On slim DVD/CDRW (onboard SATA)
Intel PWLA8391GT (1000GT)
Koutech USB 2.0 Header-Pin to Dual Type-A adapter
Patriot 4gb USB (boot drive)

BIOS Edits:
C1E option is turned off
SATA is limited to SATA2 (not 3)
Hard drives are in AHCI mode
IOMUU turned on

I used the 3ware BIOS to set up the RAID 5 with 4 drives and turned on auto carve at 2tb. Using the great script, I modified my install CD to recognize the 3ware controller and installed to the USB. Afterwards the server recognized the 2 LUNs. I deleted the second datastore and extended the first datastore to cover both LUNs. With IOMUU turned on in the BIOS I can see that the PCI passthrough is enabled and I can configure the devices. The 6 core Phenom II processor is recognized and all 6 cores are usable.

One thing to note. With the 3ware 9690SA, use the drivers on the LSI website rather than the oem.tgz module posted here. The LSI website has an update which is much newer and much faster.