Or does the hoa need to send a letter for them to be officially be breaking the lease? 

Suggest you call a loan official and show him photos.

It's truly like going back in time and the current town officials were completely unaware of all of this LOL as the old officials are now long gone and nobody was the wiser.  

I think Realtor.com is the official website of mls and you should have full access to it as a buyer right now...

I would bring the current owner with me and have a face to face talk with the building officials and get it straight from the horses mounth with the current owner being aware. 

Assuming me and the potential seller reach an agreement on price over the phone or by email, what type of document or form would I need to make the agreed upon price official?

Over the last year and a half I’ve accumulated 45 units and haven’t done any official background check on any of the placed tenants.

I agree with @Matthew PaulOne of my rentals is a 3 story house with 4 baths, it's 2 blocks away from my "Official" job. 

See the official San Francisco Office of Short Term Rentals website here: https://shorttermrentals.sfgov.org/Best,Michael Young

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