Acronis True Image Clone questions

I installed Windows 7 Pro on 2 500GB WD Caviar Blacks in a RAID0 configuration, and had a 1TB Caviar Black as storage. I recently noticed that my programs were hanging and boot times were in the 2-5 minute range which was considerably slower than I had been experiencing (system was built in Mar 2010). I tested them with the WD Date Lifeguard, the test on the RAID drives took 1 minute and  a half, the test won the 1TB drive took 22 seconds. I then benchmarked both drives with the free version of HDTune and my RAID drives were noticeably worse than the 1TB drive in every category excpet the Max Transfer Rate. The Access time for example was 50.0ms on the RAID drives and 13.4ms on the 1TB. I ran CHKDSK on a reboot and it took about 14 hours. Obviously one of the two 500’s is failing.

After backing up the data on D: (the 1TB drive) to an external, I used the Acronis True Image application to clone C: (the RAID/OS drive) and rebooted. I assumed that like other windows OS it would prompt me to boot into one of two versions of Windows, instead it booted directly to the C: drive and the slowdowns were still apparent. I restarted and attempted to set the RAID ports to AHCI in the BIOS and it failed to find an operating system. After reverting it back to a RAID device I managed to boot into the cloned partition by manually selecting the WDC 1TB drive from the boot menu in the BIOS upon restarting. As of my typing this I am in that drive (now renamed F:) and everything is working.

My concern however is that What was formerly C: is now C:  with 233GB used and then there is D: which is System Reserved 29.6MB of 99.9MB used, the drive my OS is running off of is F: with 240GB used. None of the drives has the windows icon indicating it is the system drive. My goal is to get the 2 500GB drives formatted to determine which is failing so that I can RMA it. I’d like to get the drive letters sorted back out naturally but I am unsure of how to go about making F: a bootable drive (without having to go into the boot menu every restart). Once I determine which of the 2 500GB drives is healthy I was considering cloning the OS back to it, and giving up on the RAID setup entirely once the bad drive is RMAed.

Currently everything is working fine, in fact it’s working better than it has for a few weeks now. I am just trying to get it back to normal in regards to streamlining the boot process. I am not sure if I can just use True Image or Lifeguard to wipe the drives and then format them. If I do that will I be able to set the F: drive letter back to C: and have everything go back to normal? Any help or suggestions would be welcomed. Currently I am happy that I didn’t have to do a full format and reinstall of windows and have to manually reinstall all my programs, but eventually I need to to get those two drives sorted out , one of them RMAed and hoepfully get the OS cloned back onto the healthy drive.