A big issue I have with this is that the cash randomly flips to negative numbers
If you mine lava and have a low amount of money, you'll be in the negatives intentionally. I've never gotten any reports about it "randomly becoming negative numbers", though.
and will subtract it even if you don't have enough for something in the shop.
Pretty sure this doesn't happen either. Each of the /buy, /upgrade, etc. commands all check to make sure you have enough.