Yep, the documentation UI is custom, on top of typical jQuery stuff. We looked at off-the-shelf solutions, but none of them were quite awesome enough, and it's really important to us to have great documentation, so we ended up rolling our own.
Could you turn off the CSS for changing the highlight color? I know it is all the rage these days, but it is an accessibility issue for me (and probably others as well). I use highlighting to make it easier for me to read text (it helps by eyes track better). When you change the color (especially to something garish) it substantially reduces the usability of the site for me. Yes it is just one Firebug edit away, but really I shouldn't have to do it.
Operating systems allow people to set custom highlight colors for a reason. I don't see why website authors think they know better than their users.
