There was a bug in the 2.5 series involving the Island namespace (that occurred in some common, but random circumstances) that broke some things including autolinks.
I recommend upgrading to 3.0 first, as I'm pretty sure that will fix your issue. We are only releasing security fixes for the 2.5 family now.
I had a similar problem on my other site with users complaining that important content was hard to find. It's an ongoing battle, but you just have to figure out which content your users are looking for, and bring that closer to the front. The more graphically you can set up your pages the better, because it will give their eyes a break from blocks of text.
As for the CSS not matching, I'd recommend waiting until you update to 3.0 before doing so, since there was a CSS rewrite.