So, if I refinance at $350,000 (which is at the bottom of what I think it is worth, at 4.5% interest rate at a 70/30 LTV, $6,000 in taxes, and $2,500 in insurance, the mortgage payment is $1,950/mo and the property currently leases out at $3,550/mo. 

Even if there is no lease, if it's been 30 days or more, then this is a concern.

I currently live in a house that I have a lease purchase agreement on.

The housing department has not paid me their portion of the rent since October due to the fact that I have not signed the HAP contract which looks and reads a lot like a lease to me.

I have an opportunity with a seller who is willing to do a lease to own contract for me to purchase a home he bought and is now ready to flip.

We could buy all of the land and lease them back the building for $1/year or something, they are really flexible. 

My lease doesn't specify when a late fee is to be collected but it does specify that if rent is not received after the 10th day of the month a late fee is assessed.

The lease says to pay by the 9th and today is the 16th.

This would be my first commercial property and while it has some tenants already I know these can be a bit more difficult to lease out than a 2 bed 1 bath. 

First you schedule a walk thru of apartment so you know if you want to renew them or not,, crappy house keeping,, what ever is almost good enough reason for me not to renew.Download a lease renewal form,, give within proper notice period,Raise rent if it warrants a raise, you need to market check your area..