Hello! Glad to hear you're enjoying the game.
The pillar control guide provides coordinates that raise a specific pillar. For example, the pillar maked as C would be raised by inputting number 4 & 7. The only important pillars to raise are C and D . I can see why it might not be obvious.
As for going back, Marywell loses the slime-repelling runes after boarding the elevator. Before that, you should be able to go back. After that, you can still board the elevator and go to Floor1, reapply the runes in the alchemy lab room and make your way to the cave. That said, all scenes will be unlocked at the end of the game, so you don't have to do it if you don't feel like it :)
The puzzles get a bit simpler as the game progresses. This part of the game was already done by the time we made our demo - before we received feedback about the puzzle difficulty. I apologize for the frustration!