First, you have a terrifically fun company to work for, I think. I help with industrial storage solutions, but don't get too many of these a year, and haven't had a chance to play with Pick to Light in over 5 years now.
One folder that we find very handy , is to have a "record" folder at the top level, after the project number.
Into this directory for the project, we copy all issued to client or city permitting, "record" files, such as drawings or final reports, along with a decent descriptive title and date. It makes looking for project records so simple.
Otherwise, our folder structure is a lot like yours..
Project number
- Major divisions (Proposal and quotes / Project / Management for the admin stuff life CO's, invoices, meeting minutes and contracts / Resource are materials provided by the client like their floor plans, or our initial site photes)
-- Division by Discipline or functional area within our company...
--- Division by sub project or by phase
---- Whatever folders you want to divide it into, at a minimum "drawings" and "Anaylsis" and "correspondence" are common.
Note that Major divisions include the ISO 9000 requirements that we have, so they are easy to find for auditors. things like safety, quality, management, etc.
Attached is an overview of what it looks like now. Some offices add the numbers 01_ etc in front.