Starting out the level design progress by mapping level elements and working on a flow figure.
First I tried plotting down every game element I have on paper, so things like:
Some of these make no sense and some overlap with others, but it helped a lot when I was figuring out the flow because I could see what I was missing and what I can combine for later challenges. Also it cleared my mind a lot because this is a mess even on paper.
Very in progress flow figure: