Seems like you just need an amendment stating exactly what you have above.

Amazing how the bad guys tend to make amends when they're facing jail time.

However, there was a townhall recently where they are trying to amend the CUP for the North End and Shore Dr.

You can always go back at a later time and amend your articles of incorporation after consulting with a lawyer. 

Me, as a wholesaler, of course, I prefer a buyer who is all cash, since lenders can make things very complicated and potential de-rail my relationship with the seller if the buyer blows out due to lender issues, however if it's more of a hard money/private lender who has lended on these types of properties before and realizes things may not be perfect, then I sometimes will allow my buyers to use a lender, however then we have to do an Amendment/Addendum to the contract that the seller has to sign that acknowledges it changing from an all cash deal to one with debt, which so far I've been able to finesse sellers into.

The first article has a link to the original ordinance and amended ordinance in 2018. 

His theory was agents fight less for repairs, fight harder to keep deals together, pay for minor repairs themselves vs writing amendments, etc. 

I would say just that to your agent and have them ask the seller to amend the agreement.

If they say they don't plan on getting another animal, amend the contract and remove the $50/mo.

As far as validating the rental revenue, there are a few things to consider: ideally the estoppels would be notarized; confirm the lease agreement information matches the rent roll, p&l, and bank statements (bank statement would show you how much they are actually collecting); request copies of the executed lease amendments or other written or side agreements the owner may have had with the tenant(s).