I was talking about the one next to the Goron, you can't get passed there. Wouldn't save very much regardless
There's a consistent way for the crate. Look directly at the hole and jump, and try not to let go of the Control stick. You should also give yourself some distance on the crate itself for a running start.
For that backflip, it's just memorization. For a few parts in the run, I try memorizing objects (scenery, torches) or patterns on the floor/wall so that when it comes into my view as I backwalk, it can show me when to either turn around or backflip