Depending on the buyer's desire for more "teeth", all of this can be satisfied by stipulations in the agreement that satisfy any of their reservations.

Is there a list stipulating which states require a license to broker notes nationwide?

The only way you could receive long or short term capitol gains treatment would be if you rented them for the required times as stipulated by the IRS.

We do stipulate in our lease that the included water is based off of normal use and usually add an amount of gallons/month we are including based off the number of occupants on the lease, but I'm not sure how hard it would be to get reimbursed for excessive use in the event that happened. 

Ouch,rule No 1 is no pay no stay...better move out now because the landlord will give you a five-day notice to move or you can stipulate ie make a plan to pay back what is owed in a face to face meeting at the courthouse.

I did check with the HOA and they allow renting and I'm following their specifications, however, I'm not clear if this type of rental follows the same rules/stipulations as if it were a house, duplex or any other rental property. 

Even if it was your only occupation, the IRS law/reg stipulates that its a passive activity.

IRS rules stipulate there can be no direct or indirect benefit between an IRA and a disqualified person, and you are disqualified. 

Someone should have signed off (the tenant) that the property was in acceptable condition when they took possession; our lease stipulates that by accepting the property upon move-in the tenant is accepting the condition and cleanliness of the property.

There are several stipulations (in AZ at least) that include listing the property for sale for one year based on a valuation criteria set by the governing body overseeing LIHTC properties.