Still making some tweaks and looking to get some more feedback.
Here's the new homepage. We abandoned the combined view as it turned out to be less simple and easy to read than I had hoped once there were more than 5 or 6 questions.
Here's a slightly altered section page (PHP in this case). We tried to make it so the most important things (new thread, title) are prominately displayed.
Here is a sample profile page. Re-arranged a few things based on feedback. All the basic information is displayed in the blue box at the top. Friends on Profile hack is still being used, but tweaked to fit the layout of the site. We coded a section to show the user's last 5 threads and posts on their profile as well.
Here is a "show thread" page. Our goal is to make this as simple to use and easy to read as possible. We're working to get a few more of the default vbulletin features mixed in there, but we want to do it in a way that doesn't impede navigation or make the page more difficult to read.