We organized ours to pretty much mirror SQF's system to make auditing easier. So "theme" 1 for SQF is Management Commitment. Our documents pull straight in order of SQF's system and look like this:
1.0 Management Commitment (main folder)
1.1.1 Food Safety Policy
1.1.2 Continuing Letter of Guarantee
126.96.36.199 Organizational Chart (associated with the continuing guarantee topic).
All of our SQF specific documents are "1._". After that, sanitation gets it's own "2.0" folder and manufacturing gets "3.0" and so on. I think it really helps to keep things moving in our audit, since we pull right from the book.
Our register is just a simple excel sheet that we use to audit our system as well - it's got document number, document name, revision date, effective date, internal audit date/initials, and comments. As we move through the years, we just hide the comments and audit dates from the year prior. We have more detailed change notes on the actual documents themselves, including who made the change, the date, and what was involved in the change in a table on the last sheet of the document.
I'm also working through an updated specification form that sounds like what you're looking for. The first two pages I made for ingredients/UPC/size/nutritional info. Then I've got a page for any labels, another for any case designs or case labels, and then a last page for special instructions or palletizing instructions. I'll either drop in a pdf of the box or label, or actually attach the label before scanning the hard copy to make available for other employees. It's a long spec format, but it seems to meet the needs of our account managers, as well as our production staff, which means less questions for me in the long run, haha.