Just an update. I had added the screens before boss fights back in November and never tested the game fully. Turns out I messed up and made it impossible to reach the level 2 boss and progress in the game. It should be fixed now, and you can play to the end of the game.
As for the collectables, the Info option at the title screen somewhat explains the mechanics of the pickups.
I'm aware of the other minor issues and am still working on them.