Thanks for playing.
These are all fair criticisms. There's a few navigational hints in the game (mainly the colour-coded halos and pointer particles on warp-points), but they aren't well explained.
I kinda wanted to make a mini-map that showed the rails of each room. Didn't do it due to a lack of time, but I also don't want the player to be constantly switching between the game and mini-map. I'll probably just have to do a full redesign of the organic zone. It's easily the worst area anyways.