Original Post: I'm in a similar boat as you and went ahead and and tried to upgrade. The installer got pretty far into the process, failed and reverted back to windows 7. So, no harm done. I'll try to revert the junctions I've made and see if it helps.
Update : Steps to Ease Upgrade
- Junctions and symlinks will break the install process or will hamper Windows operation after update
- If you haven't kept a record of which drives have been junctioned / sym linked, use "dir /aL /s c:\" to find junction points from the command prompt. source: wikipedia
- Clear out your hard drive and rmdir to remove the junctions and place the files back in their original drives prior to upgrading
The install worked after I removed as many junctions as I remembered, including the main one from my User directory and moved it back to my SSD drive. However, the Windows Store, and Windows Update were not working as I had junctioned the C:\Windows\SoftwareDistribution folder, which was necessary to download programs and updates from MS. The install worked and the folder was updated (now located in E:\Windows\SoftwareDistribution), but the junction link was broken during the install process. Fixing the junction fixed the problem.