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.