I haven't run the game since before the illuminati wrote the autosplitter and I think I would have to change a lot of my splits to use it, so I guess I wouldn't bother.

As illuminati said in the thread you linked, "You need an individual split for each mission/s&f (this includes Prologue)" - it just counts Prologue as a separate mission and you have to make separate splits for Prologue and Franklin & Lamar and it should work just fine.

And also "The script won't start automatically, you will need to start it. It also won't split at the correct endings, so you need to manually split at the end as well". The autosplitter just splits after certain missions, but it doesn't start the timer and the moment the last mission is considered finished by the game (so that the splitter actually splits then) is different from when we stop the timer normally.

Good luck with the runs! ;)