I think it's a mistake to assume that just because someone can program great software they are effective website designers or technical writers. Completely different skill sets.
I'm all for a re-doing the manual in more concise language (and languages other than english too). From there you could add "footnotes" for people to add in their own experiences, tips, tricks, etc. I used the program "Sitesucker" to download it all from the JJOS website. I'm sure there are windows alternatives.
I mean, even small things like listing all the manual topics down the righthand side of the page and displaying the info on the left would be appreciated. Another example is that if you get a direct link to a manual page there is no way to go back to the table of contents.
Personally, I think that archives are fine, but should be "hidden". An email alert about new version would be great too, but again it should point you to the real site. (It's a shame the official site doesn't have HTML anchors so you don't have to scroll around and could link to the exact right area) You don't want people randomly coming to your site downloading the software and then not having an idea of where to buy it or how to get more help with it!
Consider this, if your site is successful and proves to be a great resource it will move up in google rank because most people only visit the official site to DL the new version. Also, a lot of browsers let you search right from the address bar so if someone types jjos there is a chance they will get to your site without ever seeing the official site.
Your website design has some really nice touches and tons of potential. It is a bit dark (hard to make out "OS" on the download), the "glow" around links is too flashy for my personal tastes and I think the real(?) JJ logo is much cleaner, with more modern design sensibilities about it. Now, I'd try to find whomever made it to get permission rather than take it though.

Overall, it's a good start. I like the color hi-res screen shots and appreciate the effort you've put into the whole thing!
