Fred, I'm a bit confused as it seems you're jumping around a bit. I've got an EX490 which is identical to the EX495 except for the stock processor and stock hard disk were a bit different. In any case, you noted you replaced the Silicon Image driver, which only controls the eSATA port. So are these suspect disks in an external drive array? The Silicon Image eSATA can support a port multiplier up to 4, maybe 5, disks. I've got a Rosewill enclosure on my EX490 now running Windows Server 2012 R2.
If you're referring to the 4 drive bays inside the EX490, those are attached to an Intel controller.
When you say you are getting near constant errors that the drive is failing, where are these errors coming from? Do you see SMART errors during POST (you'd only see these if you've got Charles' VOV debug board)? Or are you running a disk health monitor such as Home Server SMART or HD Sentinel?
It is possible that the backplane to which the disks attach in the server is going bad. I've got SSDs as my OS disks in both my EX490 and EX487, and both use the ICYDock converter. Never had a problem with disks being recognized. I also use the ICYDock to boot the EX490 with a laptop drive when I want to run WHS v1 to test new builds of Home Server SMART Classic.
WHS 2011 will recognize the Intel controller in the EX490, as will Windows Server 2012 (including R2). If memory serves me right, they all use a generic IDE/SATA driver, so you need to install an updated version of the Intel RST driver after Windows is fully installed, but this won't preclude you from installing Windows.
If you have an external enclosure, I would recommend hooking up the suspect disk(s) to a different Windows PC. Install WindowSMART 2013 @
http://www.dojonorthsoftware.net/WindowSMART.html on the testing PC. This will read the SMART data from the disk(s) and tell you if any critical attributes (i.e. bad sectors, end-to-end errors, spin retries, etc.) are indicating failure. SMART is imperfect, but it is a fairly reliable predictive failure mechanism. It's not likely a brand new disk is failing, but it's not impossible either. It could be defective, or it could've been mishandled during shipment (i.e. dropped).
Matt