Just start over then restore from your backups. There is an issue with Windows in that if the year or date/time is off it can fail. I've run into this and as of today all I can write is "don't do that" since system restore and a lot of Windows gets sorely confused if the date/time is changed too much.
Sorry to read you have so much to do to get it working again.
I have an ASUS GA-7VAXP motherboard with two Seagate 80 gig drives running mirrored on Promise raid. I was loosing the date and time and then started getting CMOS checksum errors which finally prompted me to replace the battery. After replacement I booted and got in my Windows XP no problem. I shut down and next day when I turned back on I got an error saying 'We apologize for the inconvenience, but Windows did not start successfully..." I put in the XP disk and reloaded Windows (update not a full format as I have many files I wish to keep intact) I did the loading of the 3rd party raid driver etc..
This did not help. I then realized that my CMOS got reset so that Raid Controller Function was at ATA and not Raid. I set that to Raid and made sure that RAID/SCSI boot order was at Raid and added SCSI to my boot devices. (1st boot = SCSI, 2nd = HDD-0, 3rd = CDROM)
I still am unable to boot into XP. I removed a drive from the IDE 3 and put it on IDE 1 and booted successfully into XP where it asked me to load the Promise drive. I did and did that also to the drive on IDE 4 (by putting it on IDE 1). I reconnect my raid (IDE 3 and 4) and I still get that error. Any ideas?