He even wrote me a written statement about this, which I submitted to his insurance agent for verification 2 weeks ago, and haven't been responded to. 1) Do I just pay the guy and be done?

You must submit a request for a letter ruling to make a late election or revoke an election.Any change in the placed in service date of a depreciable asset.See sections 1.446-1(e)(2)(ii)(d) and 1.446-1(e)(2)(iii) of the regulations for more information and examples. 

what happens if I submit my offer after the due date?

If you or a trained CPA on your team can get on the phone with me for an hour to explain how certain things will be done based on the questions I submitted to your team, it would be an easier decision for me to make to join your program.

Another option could be to submit a conditional offer that each of those items are fixed before closing by a licensed and insured professional (if that is important to you).

Hello BP Community, we're having to bring an unpermitted unit in an older building up to code for a dwelling space and need plans drawn up to submit to the city.

Either way, you're going to want to make sure for both lending and your own records that your husband's company is submitting formal invoices on their letterhead for the work that has been completed for your draw requests. 

They had several trivial issues with my application (which was submitted through the engineering firm) but they had one major issue.

You can make the argument that if an investor wants it, they will submit an offer whether it is listed with a Realtor or not.

This is before you submit to the city and have to pay all their fees.