The city code officer will guide you as to the requirements. 

I reviewed Wisc tennant landlord law and section 704 of the code and nowhere did I see a limit on length of lease when it comes to going beyond month to month.

So does altering the property in such a way that it wouldn't be eligible for new FHA financing in the future cause a problem? 

According to the building codes, my lot is just big enough to build a four-plex.

Set the lockbox with a contractor code the same as you set for each deadbolt.

Would just altering my current management agreement to include items like financing, profits, and a clause on ending the partnership possibly make the most sense?

Laws and codes have always been ever-changing and always will be.

@Marc Possoff here is the zoning code published by the city https://www.amlegal.com/codes/client/philadelphia_pa/For a garage/ parking pad you will need a curb cut which will require a variance unless its on a backstreet which does not allow parking. 

What does this code mean?

Typically if it is a municipal lien/code enforcement lien it can be negotiated with the city after the violation is corrected.