Tenants pay for gas and electric, owner pays for water.

For example where does water drain on the property.

I painted it, redid the floors, put on new doors and hardware, fixed all the existing issues (leaks in roof, toilets not working, sinks leaking, water damage on exterior and upgraded the panel to a 220V) What was the outcome?

There is significant water damage in the kitchen and also mold (possibly from over time, but not sure).

I'd just run your numbers on the new development i.e. how much can you get land for, building permits, water/sewer hook-ups, etc. 

The problem is that there constantly seems to be fees being charged to me an example of this is in the contract  there is an additional 100 dollars allocated to sewer and water that the tenant automatically pays every month with rent and anything outside of it should be billed to the customer (there is no specificed time when this will occur on the contract) but it appears to be billed to me and after speaking to IIP it's like they made up rule on the spot stating that after 6 months all of the additional utility fees would be billed to the customer and in the meantime I am being charged for it.

Commercial space rent in the area for similar properties is $3000-$4000/mo but property taxes annually are $25k+, insurance $6k+ and other expenses such as trash, water, heat & electric, etc. 

If there is landscaping that you can add where, once established while you live there, requires very little maintenance and water, then do that.

Tenants pay for gas and electric, owner pays for water.

And very important: most of the fresh water in the world.Also, MN has become landlord-unfriendly.