mizarchivist

We had similar issues with PBWorks when we investigated it; the featureset was a bit too complicated to deal with, and I wasn't a fan of the folder structure. Have you looked into Drupal's Book module? It comes with core, and it's fairly robust, although not the most elegant. It gives you the ability to sort pages in any heirarchy you need them, and there's a separate navigation that's automatically set up for books - and you can easily customize book pages to import files, etc. The only potential sticking point is that some of the files you have in the /sites/all/files folder are pretty large; we'd have to deal with the hosting company again to get the upload size larger than 30mb.