out of curiosity; If booting to safe mode what is windows hanging up on? It may be a simple repair issue. Having a 'duplicate' OS will not cause this (whether you mean a pirated OS, or having a duel boot system). Inserting a windows DVD and running the repair option just might fix your woes.
Either way, what foscooter suggested will work, and is probably the easiest way to do this. Just be aware that you will be running in RAID mode, and will have to re-install your OS (or pay for some good imaging software) to switch to IDE or AHCI mode.
This would be an excellent time to move to an SSD