Long story short. Had to run chkdsk /f on a D: drive of a 2 volume (C: RAID 1 (system - ok), D: RAID 5 (data - problem)
LOTS of orphaned files which I can pretty much handle from backup, but now the Connector for POP3 mailboxes service is stuck in stopping state. I tried restarting the information store, etc but it doesn't take. Also the POP3 connector that used to be there is gone now.
The rest of the exchange system is running and it looks like if I could get the POP3 connector recongifed, I could get by.