Would anyone recommend using the other functions? The tool author already describes their uses, but I am unsure on whether I should use them.

There are a variety of buttons and functions which look like they can be of help, but I am not entirely sure I should use them because the tool author only instructs to use the 'FixScriptInstances' function as that one removes the orphaned scripts.

Second thing is about the savetool itself. Must've gone wrong somewhere do you think I should just clean using savetool like normal or try to update from USKP to USLEEP properly? (I still have the save files using UKSP) which is weird because literally no one has this issue and everyone updates hassle free. However, surprisingly, said mod is USKP, as I replaced it with USLEEP. Unsurprisingly, the orphaned scripts come from removed mods.

'Fixing' them through savetool should be theoretically be of some help, but there are a few things I need to ask Started noticing some random CTDs (none of them save crushing ones, thank goodness), so I decided to take a look at my save through savetool, and lo and behold, I have orphaned scripts.

Skyrim save game cleaner mod