Depending on where you hit a checkpoint, you might still be able to progress. The shotgun can open up some new passageways (the green netting). If you post a screenshot of where you got stuck I might be able to help you out further.
The green netting was the piece I was missing. Thanks so much for the reply! Just finished up playing through and it was pretty dang enjoyable. I enjoyed how you structured the world with everything being in the same "level", but wrapping around in different ways after you unlock the different weapons.