I thought he would have to replace the whole thing but you don’t have to unless you want to completely upgrade to a newer refrigerant.

Looks like they did a complete building upgrade during that time period, but now he has to move. 

I mean, there has to be some level of increase for rent if you upgrade the flooring, right?

The home has a 100 amp panel and I plan to upgrade to 200 amp.

Using a short term HM loan, as @Kaelyn Motzel suggests, would only make sense if you (a) can get the house priced low enough and (b) the house seen some amount of renovations/improvements/upgrades to bring it up to full market value after said renovations (ARV). 

I've only had one system go bad after I made the upgrades. 

No but usually upgrades like flooring and bathroom upgrades should have more of an affect than that. 

We are slowly doing some upgrades to the house and yard that might add value to the right person but really this house was turnkey, ready to live in and we are just letting our room mates help us cover the costs.

You either need to find a property that has the potential to make more revenue than it is currently making (through upgrades or better marketing) or be willing to speculate that rents will increase over time and it will eventually cash flow (something people do all day all over here in CA, but I do not recommend)  

We have two under contract now (6 and 11 unit) that good properties that cash flow, but have upside with raising rents and doing upgrades.