Talked to county to figure out tax situation and any other misc charges that may change based on purchase price3.

Don’t wait to be “surprised” when you’re city suddenly introduces a 3% rent increase cap and suddenly the max you can charge only goes up $18/mo every year. 

When I first started investing, I paid close attention to the cost my GC was charging per unit.

Current rent i charge him is $975, basically just paying my mortgage for now.

So you'll be unlikely to find any legal recourse through the courts, and in fact you may end up having charges brought against you (most likely "obtaining a good or service using a false name"). 

In CA, you can't charge more than 10% without using a broker to arrange the financing.In my opinion, people should use seller financing in cases where the property is not easily financed to regular buyer or they really want to hold the note for cash flow.

As @Russell Brazil stated, you legally cannot charge a pet fee or pet deposit.

Because of that you should not charge either party.  

The reality is the opposite - if it's not in writing then the PMC doesn't have to provide the service or can charge extra for it!

To me this feels like purchasing a car from someone, then the DMV all of a sudden says "Sorry, we were under charging the previous two owners the incorrect registration fees for the last few years, you now owe us thousands of dollars."