I'd like to second the nomination of Moodle (http://www.moodle.org) to solve some of your problems. I use it for home school purposes, and my students enjoy it.

With Moodle, you can create class groups where students can blog about the class and get points for leaving comments on each other's blogs, etc. You can re-use class material (including student-generated material) for future classes very simply. You can create as many wikis as you'd like -- even multiple wikis for every class. You can use discussion forums, offer a personal page for each student, etc. It is so flexible. It can also import course files from other popular e-learning platforms like LAMS. You can post your notes or other info all at the beginning of the term and indicate the date it should be visible on the site. You can create individually randomized tests and quizzes.

Moodle also makes it easy to upload pictures, video, and other multimedia, so you wouldn't need to have the FTP or SFTP ports opened. It's all done via HTTP. You can post audio files and video files, and the site just automatically makes it easy for people to click and play them. What if you were to record your entire class session and post snippets of it next to the notes for a particular idea so you can explain complex concepts? That could help auditory or visual learners.

I'd skip the PDF step and just upload JPEGs or PNG files that are slimmed down with an image editing program like The GIMP. I use Linux, and I know you can also quickly use ImageMagick from the command line to convert files to lower resolution images. You can get a Mac version of ImageMagick here: http://mac.softpedia.com/get/DTP-Prepress/ImageMagick.shtml

You can download tons of Moodle modules to do as much or as little as you'd like from the Moodle site. New modules are created all the time. If you need help figuring things out, you can post a question to their discussion forums, and tons of people will help you out.

It's pretty easy to deploy. You could either host it at your own home, or anywhere on the Web. It just works. Maybe your IT folks would let you host it right in your classroom on a cheap PC and link to it from the main District or school Web site.

Another tool that is not really education-based is Drupal. It is also pretty easy to deploy and it is totally tweakable without too much HTML/CSS/PHP knowledge. In fact, I think 43 Folders is using Drupal from the looks of it.

Most Linux-based hosting providers have the LaTeX libraries loaded on their servers. I think Moodle and Drupal can make use of that back-end to display LaTex images.

My only complaint about Moodle is that there are so many things it can do. It takes a while to comprehend the whole picture and pick and choose what functions you want to use. It is easy to get lost in all the details and take months to actually get a functional Web 2.0 experience working. My advice is to start slow by only deploying your highest-priority tools and add additional tools at a later date. As Guy Kawasaki says, "Don't worry, be crappy." Just get something up there and let your students start using it.