I'm experiencing similar difficulties. It can't find the remote repository and I need to import a previously saved QAWAPP file.
Once that is complete I'll check out all the objects from source safe again.
If anyone is are upgrading to 2009, before you begin...
1. export the global repository as a safety precaution
2. check in your repository to your companies version control software.
CHECK YOUR upgrade file located in your global repository folder for completion before going on to anything else. the file is names upgrade_MM_DD_YYYY_HH_mm_PM.log. At the end of the file you should see
Upgrade fully completed on Friday, December DD, YYYY HH:MM:SS PM
Below is what happened to mess me up, please feel free to post your troubles with this upgrade.
I have about 2500 - 3000 objects in the global repository. My machine only has 1GB of memory. A Slow machine for so many objects.
When the installer dialogs finished at 10:48AM there was a process counting the objects in order to finish the repository upgrade yet there is no status dialog or window saying something is running in the background.
Good practice dictated that I should reboot after upgrading or reinstalling even if the installer doesn't ask me to do so. So at 10:55 I rebooted which resulted in the repository upgrade being hosed. I had two directories ending in V4 and two logs associated with the upgrade.
The second time I let everything run until I saw the log file state it was complete and I had no issues.
I spoke with support and requested a status or progress bar of some sort to indicate a process is running.