Thanks for the response. here are the answers:
This is Windows 7 64
-Did you make sure the drive cables actually connect to the MB?
Yes, they appear to be connecting, When removing the back cover it does look like they are making a solid connection from what I can tell. Also, I changed the using info from this blolg , no luck either and now my DVD drive isn't showing up. Essentially I enabled AHCI in the BIOS. Nothing.... still
http://jonhoo.wordpress.com/2009/11/09/hot-swapping-drives-in-windows-7/
-Are you connecting them before or after booting up?
I got the entire machine up in running, installed the OS on the new SS drive and once everything seemed solid I tried putting this hard drive in. One thing I didn't mention is this was my old hard drive from before the rebuild, it already has Windows 7 on it. I didn't expect to have this as a second choice for dual boot without making the necessary changes to the boot loader but I did expect to be able to browse the folders.
I am going to try a second drive which was only used for storage.
-Usually, the hot swap option lets you insert and remove drives as a storage device. Are they properly connected and formatted?
This is what I expected as well, but I am not too concerned with really using the hot swap function. 99% chance I will never hot swap any of these particular drives. As far as them being connected and formatted, none of them are new drives and they were all in use prior to this rebuild. One has an OS, the other 2TB was for additonal storage.
EDIT: I went ahead and hooked the large 2TB drive up directly to the MOBO without using the hot swap drive and I could now see the drive in Windows, however when I tried to access it it staid "Access Denied." I enabled the drive via Computer Manangement (Windows 7) then restarted the machine; I then got an error at restart -post stating "Unable to Load Boot Sector." I turned the machine off, disconnected the 2TB drive restarted and it all came back up. This 2TB drive never had an OS on it?
I am confused now...