So, after all of your help I have started making progress and I wanted to share it with you and also get just a bit more advice. I ended up talking to a guy in IT here and they had a MAXconnect tray bay so it turns out I didn't have to fabricate my own thing after all. Good timing on my part!!! Saved effort.
So I can now confirm a few things for people out there.
1.) If you are looking at the MaxConnect bay mods for adding hard drives I say that they are well worth it. It is a custom fit CNC'd 2 part aluminum assembly that is very rugged and you can mount two 3.5 in hard drives below the optical (see photo) or if you take out the optical can get 4. I did a little experimenting of my own and by drilling two more sets of holes on the T-mount for the optical drive it is actually possible to get FOUR drives into the lower optical bay-two 3.5 in drives and then two 2.5 inch drives hung upside down on the lower 1/2 of the mount + the optical. So, if you have access to a drill press you are set. I don't have any 2.5 in drives I wanted to mount in there but I did drill the extra holes and can confirm it is an option just so you know. See pics, I threw a 2.5 in there so you could see it.
Moral is you can get an optical, six 3.5 inch drives, AND two more 2.5 in if you drill it.
2.) I bought the RocketRAID 4320 and there are NO issues with OS X 10.5.6 and the EFI update v1.3 as previously reported. The update was successful, you CAN boot from the card (I have done it now), and the web management software is actually quite easy and there were no issues reinitializing disks in legacy format back to incorporation in the RAID array. So far I am very impressed with the RocketRAID.
Users should however be aware of an unsaid restriction on password length with the web-based configuration tool. It is limited to 8 characters and so I was CLUELESS as to why I couldn't get access to the card management but Highpoint's tech support sorted this out fast after calling them though it took a while since it is a oddity. Email support was slow but a phone call got me right in.
So, just a review on the Specs and what decisions I made.
Mac Pro 2x2.8 Ghz, 6 Gigs Memory
1, 300 Gig Velociraptor OS system disk (I decided this route would be "safer" in the event of an update making the card inaccessible. Plus this thing screams and now is just the OS disk).
5, 1 Tb Seagate Barracudas (all ES.2 but 2 that will be replaced soon) connected to a Highpoint
RocketRAID 4320 card via
MaxConnect SAS/SATA Link (to reach the card from the iPass cable.
Critical files (Research, Photos, OS, etc) are backed up by 2 terabytes in an extra USB enclosure. NAS will come in the future per your suggestions, but this has me covered for now.
So, where I am now is that I am doing 2 tests (following Nanofrogs suggestion) I am setting up a RAID 5 + HS and going to test performance and then I am going to do the same thing with a RAID 6. I realize that I may take a small bit of a performance hit on the RAID 6 but 2 disk failure seems like it is desired over the Hot spare. We talked about this before but any additional thoughts are welcome on which to do.
But, what I really wanted suggestions on is regardless of RAID 5+HS/RAID 6 it will be 3 terabytes in the Array. The default Block size is 64k and the default Sector Size is 512B. Do you have any suggestions about how these values should change? Or is it fine to accept the defaults?
Lastly, what is better - Write Back or Write Through? I have my whole system on a APC 1300 battery backup so I have about 15 minutes of run time so is Write Through really needed?
Thanks again for all the help. I wanted to include the pics in the event that anyone would benefit. Cheers! S-