Restoring Database After Upgrade

My team is currently trying to migrate YouTrack 5.2.3 to the most recent YouTrack 6.

I followed the steps from https://confluence.jetbrains.com/display/YTD6/Upgrading+YouTrack+with+MSI+Distribution.

1) When following those instructions, my YouTrack instance improperly installs to port 80, which is in direct conflict with our previous installation to port 85.
2) We are backing up to a remote server and cannot add a local machine user to the environment. Since YouTrack 6 runs under JetBrainsYouTrack user, we are unable to backup. When we try to change the service account user, YouTrack 6 fails even to load.
3) Because the data directories for logs and database changed, our current setup does not properly migrate and we have to add the user manually to the folders where the data already exists.

Seeing all of these problems, we thought we would just do a fresh install and restore the database. When installing a fresh instance of YouTrack 6 on my local machine and following the restore steps from https://confluence.jetbrains.com/display/YTD6/Restoring+Database+from+a+Backup:
1) My local machine forwarded me to our current v5.2.3 instance running on a vm on a server. I can't get to any configuration options because they are all contained in my local instance...
2) I can't see if the issues and project restored successfully, so there's no way of knowing if running through this procedure will leave us with a working installation.

Getting these VMs snapshot and restored over and over is controlled by another group. What should I be doing for this situation?