That's interesting, IRS seems to have adopted the attitude of "if we can't trust you to know the $750K limit, we can't trust you on anything.  How do we know the loan wasn't taken out for a trip to Monte Carlo?"  So I think you're on the right track with the closing statement, especially if the address is the one on the tax return.  And I would include a signed taxpayer statement that the loan is on a qualifying residence.  

When you write "they sent a response," what did they ask for in the first one, and what were they sent?