Yikes, wish I could come up with some fix for you. If you're using integrated (on board) RAID controller, the new motherboard probably has a different controller or significantly different revision of the same controller. That could easily lead to data corruption--if you don't first break the mirror, connect to your new motherboard as standalone drives, then rebuild the mirror under the new controller. Did you try going back to IDE mode and take turns connecting each drive to SATA port 0? Unfortunately, in this scenario corrupted writes were probably mirrored across both drives...
My system and data volumes are also RAID1. But, as you can see it's only helpful in the case of a single drive hardware failure and does nothing to protect against successful writes of corrupted/infected data. That's why I keep multiple generations of system volume image backups on an external drive and have multiple layers of malware protection. Even then you're vulnerable to a disaster that damages all drives. That's why more people are backing up to the cloud as well (online backups). A lot of trouble to be sure, but worth it if your data is important to you.
Of course this isn't going to help your current situation. Maybe a computer repair shop can recover at least some of your data.
Thanks for the input, but I'm good now.
My drive 0 was trashed but I was unable to boot off of either drive (like you said, probably mirrored the corruption to the good drive), so I changed the bios from RAID to IDE, unplugged drive one and reformatted and reloaded drive 0 from disk.
Then I plugged drive 1 back in and it came up as C & D drives and lo and behold all the files on drive 1 were still intact.
Scary movie but a happy ending.
Don't think I'll use raid anymore, just stay at IDE and use D Drive for backups.
Glad to hear things ended on a happy note. What do you use for backups? Just curious. My current favorites are Terabyte's Image for Windows (affordable, reliable image backups, good support and generous 3 PC license) and Paragon backup products for the full gamut of image, file backups and partition management. Used to be an Acronis fan, but recently they've been putting out buggy software that might get fixed about half to two thirds of the way through the artificially ru$hed annual development cycle.