To be honest this project while coded well has become messy and disorganized, I'm wondering if it would be easier to re-code it with these latest features as opposed to trying to re-factor it.

I think a recode from scratch would be a bit extravagant, but it definitely needs a refactor which is what I've been pondering on for the sign based memory stones. Maybe let me know how you would design the code differently, then we could discuss that and refactor the code into the new design.