I suspect that you have two unrelated issues here:
1: Your RAID set was degraded.
2: You have a corrupted filesystem.
Note that 1 should not have caused 2. Sometimes 1 is detected at the same time that 2 is detected: while trying to reboot a machine.
My advice is:
1: Image each of the remotely working drives with a data recovery tool that can retry and continue on bad blocks, using a machine that knows nothing about your RAID setup and won't try to fix it and/or a forensic read-only drive adapter. I simply use ddrescue on linux for this. This way, whatever happens in the raid / filesystem recovery later, you know you can't make it worse, and can always try something else.
2: Rebuild the array with a new drive (make sure you know which one was faulty and replace it). If you have multiple bad drives, try various combinations of them, and restoring the backup images onto new drives.
3: Install Windows again using rescue/reinstall mode and/or just boot in last known good mode if you can.
I would expect your data recovery experts to be able to fix this. If not, they certainly shouldn't have made things worse for you, so hopefully the steps above will work.
Sounds like you have some crucial data on there in the VMs etc. But, as jscott says, do bear in mind what the data is worth in terms of your time and effort, and what it might be costing the company to have the machine(s) down. Don't spend too much time on it. If possible, put a new system in place, or the old machine with new drives, and recover the old drives later.
Good luck :)