no, nothing was changed. In fact, I tried the repair and it failed configuring services. So, I suspected app identity. I ran the aexconfig /svcid command. We still had problems.
I also noticed in sql logs app identy trouble with iis app pool identities so I switched all to network service. That didn't fix it either.
I then ran an upgrade to mp1. Sql server cpu spiked then and we were getting i/o erros in sql logs.
At that point I decided to just rebuild. We've wasted too much time.
After uninstalling, I noticed a lot of space was still used in IIS. Logging was turned on and we had 80 gigs of log files. I don't know if that was the problem, but I know it isn't good. I've cleared the logs, turned them off, and reinstalled smp. That is my fix at this point.