Preventing flip flopping from online to offline should help fix a bunch of issues. To prevent a lot of cheating with the online version, the source of truth for the data should be on the server. There should also be "watchdog" scripts that look for anomalies on the server data. Eg. data outside 1 or 2 standard deviations or fast rates of change to resources or money. Every MMOG has fairly sophisticated anti-cheat things set up to prevent hyper-inflation and cheating.
Building upkeep is fairly brutal now though. Instead of it being money based could it instead be resource based? That would normalize the repair costs during bouts of inflation / deflation. Right now my repair bill is about $5M every minute or so. I'm not sure if it's possible to continue to pay that bill based on all my buildings income now (even selling things on the market to help raise the money). I will probably just lets the buildings fall and build new ones.
My YouTube tutorial series: https://www.youtube.com/watch?v=Tfw_-RB6D-Q&list=PLHw_EJXYsdHgSUAzwqvtfgpoBDm16flcP