Mount the VM's disk to another Windows 2000 VM, power on the latter, and verify that all system files came over. It's possible that all you need to do is change the partition number in the boot.ini.
Hardware RAID systems are supported-- Converter will see one logical disk and clone that. Converter may have issues with some software RAID, particularly Windows 2003 Server, in which case you may need to dismantle the mirror to be a single disk prior to cloning.