I have 2 major questions regarding running this game. The first is if running the fan translation would count as its own category due to the pretty large time difference? Not that it really matters that much, I'm more just curious. The second is regarding NG+ runs. Are there any official rules on things like the second file, such as a max level or certain equipment that can't be used or something?

You can filter the leaderboard so that only English runs show up. I don't know why they don't show up by default. You'll have to talk to VB about that. But yeah, it pretty much counts as a different category.

For NG+ runs you can have anything as long as you can get it in a normal playthrough. For example, you can't give Salsa stuff you can only get in Chapter 8, but anything up through Tanetane Island is okay. Level doesn't carry over, and neither does equipment for anyone but Salsa, Lucas in the first Mole Cricket fight, and Duster in the Reconstructed Caribou fight (headgear only). Lucas and Kumatora should have every PSI ability they learn, but you don't need to go past level 60 for that.

Question about the ILs - since Chapter 5-8 are after Chapter 4, which is your first chance to grind Lucas up, is it hypothetically possible to start a Chapter 5 IL at Lv99 and still have it be accepted? Not asking because I think I'm crazy enough to do that, but I'm just wondering how submitting these would work when I get around to running M3.