Probably not what you're looking for, but I did a CAD 7.x upgrade to 9. I didnt even bother with the flat file and just completely started over. I did a stare and compare for workflows and the desktop administrator web interface. It wasn't that bad, but that depends on how crazy your workflows are.
According to the CAD Install Guide on page 40, it advises you to install SQL and to go through CAD setup with a local user (not domain) that has local administrative privileges. This user must exist on both PGs and must exist on the Distributor that can also read the AW database. Make it a habit that anytime you're going to do something with CAD on this server that you log in as the aforementioned local user.
If you follow the install guide to a tee, you shouldn't run into any issues.
