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FAQ
This is a quirk of the Mod Manager's custom file handling, when the Mod Manager is started it runs the uninstall cleanup to ensure no mod files are left over in the game's files. Normally, this doesn't take long at all, but when you have a few THOUSAND custom files (from Voice Packs or Custom Music), it DOES take a long time. Give it a few minutes and it will eventually finish the process and open as normal. Randomisations without Voice Packs or Custom Music (or with only a small amount of Custom Music) will not cause this problem.
Technically yes, although the method to do so is slightly unorthodox. First, install the mods you want to have randomised then, while the game is still open, run the Randomiser the way you want. This will cause it to also pick up the modded files and include them in the randomisation process. Just make sure to load the resulting Randomised mod with a higher priority than the other mods to ensure they don't overwrite its edits!