Active Directory Domain Rename, ran /clean too soon
I'll preface this by saying that I've never run /clean early and I've never fully inspected what bits /clean flips under the hood. That said, I have done a large-scale domain rename in a 10,000+ object forest, and it's a delicate process. I wouldn't want to rig up a workaround that will leave you in an unsupported state. Instead, I'd definitely restore your DCs from backups as well as any other servers that did reboot twice. Then start over with a clean slate.
Sounds like it is time to do a restore from your good system backups.