I think I figured out a bandage fix for the bug where the game gets bogged down by having too much Mana. It doesn't fix the core issue, but it helps.
Make Mana-related items always useable, but, when they are used, do a check for surrounding Mana, and if it has none, give a 0x multiplier to its effect. It doesn't help the fact that the algorithm is extremely processing-intensive, but it makes sure that the game only actually does the check when necessary, whereas right now it does it constantly.