I feel I should update the existing lease and charge accordingly for the extra animal and adult living there , not sure what to do anout cat door ?

They will probably send a couple of officers over.Be ready to accept custody (vs. ownership) of any firearms (or they may do that).Look for any pets and either adopt them yourself or call a No Kill Shelter: https://www.nokillnetwork.org/d/Wyoming/PCAS--Park-County-Animal-Shelter-(Cody)~9915/Look for liter boxes, doggie doors, pet bowls, pet toys...Pets hide in closets and under beds.

Now the rates are low enough that it is probably worth it to eat the prepayment penalty and refinance. 

Pro and cons for keep the property:pro: 1. we are not losing much money on the rental property2. although appreciation increase ~5% for the past few years, potential is good3. familiar with local, we know real estate/loan agents, handyman, friends could help us handle any cases.cons:1. we could get tax deduction to sell it next year since it qualified for our primary house.2. remote management is frustrated. but hire manager to manage it almost eat all our cashflow2. the house is too large, not a good invest property for 5% increase per year, cash out and invest in something else MAYBE betterIt really cause me headache whether or not we should sell the property, it is on the line of making/losing money.

It's a completely different animal for sure and has its own set of problems (some mentioned previously) but the cashflow aspect is night and day from long term if it's run well.

Taxes are eating me up...

However, you as the owner have an obligation to make sure heat/hot water is working but all the while they can break things and making formal complaints about the condition of the home that will be documented against you.Unfortunately you will likely have to eat some sh*t pie and let them leave.

With the increase in emotional support animals, I'm considering raising my rent and requiring a cleaning company once a month or bi-weekly.

But It would only eat up $475K of the reinvestment target and would need to purchase another $425 K or so if you want to defer all tax.Yes, as long as you own the replacement you will continue to defer all tax. 

@Allen MoyeOne thing that immediately comes to mind are wood eating insects.