I've wanted to scratch this itch for years and keep putting it off. Your desires don't look too far off from mine. (I do want a relational database-based index, and I'm fine having encryption handled by the filesystem.)

For now I've been scanning the documents and storing the paper copies in boxes in the order they were scanned. My eventual hope is to import the scans into the mythical document management system, categorize the documents, then go back thru the boxes destroying any items that I don't absolutely need on paper.