The cause of your stutters may occur when your game is saving and you have a lot of cached_discovery in one of your profiles. This can happen by changing game versions or swapping (map) mods on and off on the same profile.
You would need to decrypt your profile.sii and profile.bak.sii in every profile folder you have, and look for cached_discovery:, then delete all numbered [] entries and set the first line to 0.
You'll want to change it from this:
to this
Keep in mind that these cached_discovery may be in the hundreds of thousands. The highest I have seen myself before is about 260.000 entries.
Since this list will span the entire rest of the file, you can double-click on the number, then Ctrl+Shift+End, then while still holding shift left-click behind the last entry to highlight all rows. Then simply press the number 0 and you should get the second screenshot above.