I am interested in doing a SH game for a 12 hour but would like to snowball that into other categories that may require multiple clears on the same file.

Am I allowed to run Any% using a clear file as long as I don't pick up NG+ content or am I required to start from a fresh save/New Game option?

From what I understand:

1: "New game" at menu, pick Easy. NG+ is always on Normal or Hard, so obviously no reason to load a previous save. Keep in mind if there's another save with your controls changed, it'll default to those controls, if I remember correctly, and you don't have to reload the save or anything.

2: I forget if game data checks for a save or if it keeps track in a separate place like 3, but NG+ items will always be there except for a fresh install. They're all out of the way anyways.

3: New Game is separate from Extra New Game, ezpz

4: Same as 1, except it lets you choose any difficulty iirc, so New Game is always best choice. NG+ does add costumes, but I think there was something about a cutscene or two that you could skip on NG+ that was unskippable otherwise, so until someone gives more detail I think "New Game" is the consensus.

0: New Game, loading a completed save adds all the NG+ items to inventory

Homecoming: New Game, and I believe it's generally agreed to stick to normal costume, if only because we don't know for sure how the different character model would affect clips and such. (I swear clipping is harder in Pyramid Head helmet.)

Shattered Memories: Starting from a "NG+" file only adds the UFOs around town and keeps the options you set before (tutorials off, subtitles, etc.) except for the option to play voice calls through TV instead of Wii remote. You can set all of these before starting the run on a new game file, so there's no practical reason that a "NG+" file is an issue.

Downpour: New Game/Easy. An interesting caveat about this is that if you have punched in any of the preorder bonus codes, given with the game on release depending where you bought it, Gamestop/wherever else had their own unlockable weapons (all of which aren't that great anyways). Deleting all of your saves won't undo putting that code in, the time I tried to wipe it I had to completely uninstall the entire game and all saves and system data. Basically acts the same as SH2 for our purposes anyways, it's a goofy weapon you have to go out of your way to grab. I thought it might have implications for runs where if a preorder bonus weapon was OP you wouldn't actually be able to go to a locker and have to put in the preorder code; the locker would already be open, so I guess it'd be a 10 second time save or whatever. That'd all have to be for debate, I guess.

Sorry for the essay, figured it was worth a quick writeup.

edit: Also, all of this should be listed under the rules on individual game category/run pages.