In this category, the Back in Time glitch, and all its derivatives, are banned. All other glitches are allowed. This also means the file setup doesn't matter; all you need is a blank Hero Mode file in one of the three slots.
Your blank Hero Mode file needs at least one Ancient Flower (to repair Scrapper); if you want to do the upgrade to Quick Beetle, you'll need as well:
Ancient Cistern has two routes depending on the version you're running. Both possible routes follow.