So I deleted a couple of crappy misc category runs from my profile the other day and now I have no runs whatsoever. Not sure why, anyway I can get the ones I want back?

That depends on whether you're on NTSC or PAL. The way NTSC does it doesn't work on PAL, and I imagine the converse is true. I can throw up a video guide to PAL if needed but odds are you're on NTSC. I can't speak for how easy it is to do, but you should get a good feel for it by watching jcool's run.

I'm not aware of a frame-perfect fast strat on folders? What's that? I was just talking about getting good walls/bounces and saving like, up to a second with a good stage.

Yeah, there are a few strats similar to this, but they're just not consistent enough to warrant that level of risk that late in the run. Besides, most runs on the leaderboards, my own included, can save plenty more time on the stages around quick turn (fluctuation, folders, linear seesaws and birth).

Could someone clarify what the ISO loaders bit in the rules means? As a guess it sounds like running the ISO on a softmodded wii, but I'm not sure (plus that seems like an odd ban when emulated runs are allowed).

You can set your splits to whatever you like, there's no required set up. Typically, for glitchless, runners have a split for each gym leader, the champion, and often for the 2nd Briney boat trip, just because the time between Roxanne and Wattson is quite long, and it splits them up nicely. However, feel free to have a split wherever you want, I personally utilize livesplit's subsplit plugin, and have many subsplits within each split, one for nearly every battle, just because I like having an accurate picture of where I lost/gained time.

Pictures of the final time aren't proof enough for pokemon runs, however you could just point a video camera/webcam at your 3ds while you do the run. As long as the quality is good enough to be able to see what you're doing, it will be fine.