You can actually move your Documents drive to another partition in the settings I believe or create a junction/link between the mydocs folder and the other drive
Thanks Pickysaurus. I was able to move my documents folder and now I can use Hardlinks. Unfortunately, this still doesn't solve my issue referenced in the title of the OP "Uninstalled mods showing installed". In the script merger some, but not all, of my mods are showing script conflicts eventhough they are ALL uninstalled. Weird. I wrote a bug report about this yesterday, so it can be addressed in that report.