My mentality is that if I get one actionable item, it pays for the course. 

One must register the vacation rental unit, pay applicable fees, submit a current license as a Transient Public Lodging Establishment (“TPLE”), and provide other required information.

Just trust your instincts on this stuff...which is why you went here to check. 

Make sure you pay attention to the comps to see how you need to rehab your properties. 

When will they pay you and provide reports?

They are still paying but very late each month, so I'm afraid of them becoming no-pay tenants down the road. 

If you have a repair agreement in place then you need to trust that the seller will get it done and order your appraisal.

Should I require both of them to pay application fee or only one fee?

If you do pull out money from the HELOC, have a plan to pay it back within 18 months.

Obviously, if the tenants fail to timely pay rent, you can enforce their obligations with a notice to pay.Your question is legal in nature, so I recommend that you consult your landlord or FHA attorney in your state about it.