Don,
Thank you! We submitted our response like you suggested. We've been trying to Google this problem but I guess we're the only ones that are willing to admit it's happened to them!! It's super duper obvious that the pricing isn't what we intended since it's not what the solicitation told us to do and the clarification we received told us it could "remove us from consideration for non-compliance with the instructions" and for failing to provide a document to explain why our pricing didn't match the instructions. The way the RFP read was pretty much do what we told you to do for pricing or tell us why you didn't. So why would we not do what the solicitation says and not tell them why if we know that would remove us?!
The closest thing my partner has been able to find is a court case that talked about a Contracting Officer who didn't allow someone to submit a document after they found that the document was a copy of a different document rather than what they wanted submitted and the Contracting Officer was wrong to not allow it but we can't find that case again