I haven't been through an initial desk audit, just recertification audits, but with less than 1 week to go, here would be my advice.
Findings: In general (individual auditors grade differently), SQF will issue Major findings when you have no policy of any kind to support a requirement, and minor's when you fail to either meet the entire requirement or fail to follow your policy (e.g. the paperwork is missing, or you haven't been doing an inspection you said you would). So, very quickly do a top-down review of module two and decide whether you have a specific written policy in place that addresses the intent of each requirement, and you can effectively avoid major findings with ease.
Examples: Your internal audit program and CAPA program are excellent examples of verification for a ton of different requirements, make sure you use them with a wide brush to verify systems are working and effective.
If you're using spreadsheets for any logging or trending activities, print out examples of recent and well organized weeks of use, with bonus points if they helped you identify a trend you're now taking steps to improve.
Don't oversell, be honest about your programs and their implementation and approach everything from a risk assessment perspective. See example:
Auditor: The policy says you'll review labels as they come in, do you have records to demonstrate that?
Supplier: You know, I wrote that SOP as we prepared for certification but implementation has been tough and I need to make revisions. We realized that, because our company doesn't process any products with allergens, label review isn't posing a food safety risk, so we can probably do an initial review when proofs are created, and then just work with our label supplier to make sure they supply only the current revision as part of our supplier approval program. After all, once created, the words on the label cylinders/plates can't change on their own, so the only possibility of an error would be from accidentally printing an older revision.
Auditor: okay, that makes sense, but you need to follow your written procedures.
Supplier: Of course, and I'll make modifying that SOP to follow current practice a priority.
This violates the "do what you say" idea of SQF, but especially in small companies that may have only 1-2 QA folks, making your way around to updating SOP's (especially since these are first drafts) is understandable and in good faith if you've provided a risk assessment. This approach is not appropriate for things like sanitation.
Looking at the code, since you aren't yet certified, it looks like they'll just wait to schedule your facility audit until you have completed all the corrective actions from your desk audit. No specific time limits are specified.
I wouldn't sweat it and treat the desk audit like a paid consultant is going through your stuff to prepare for your facility audit. Make sure you are prepared to explain how you meet the intent of the code if you have a unique procedure/process/product/facility, and be prepared to defend any risk assessments you've made with historical company data that is demonstrable, e.g. don't just assume "it's unlikely", be able to say "it's never happened in our facility".