In order to run 100%, you have to start on a clean file. If you want to start doing one of these runs after playing through the game or if you're resetting a run, this video will show you where the save file is if you want to delete it to create a clean file, and also how to reset one of these runs quickly while retaining the clean file.

(This guide was originally made for the World 1 Remaster, but this game shares a similar engine so the instructions are largely the same)