The overlay seems to have been built to let you switch pages quickly without scrolling all the way down a long article but since the iPhone lets you scroll quickly to the top, all of the controls could go there and be fixed. It could simply be the bar that's there already but with 6 or 7 buttons like the ai logo button and would be:
ai>ai full>headlines>iPhone blog>Mac blog>search> arrow to page 2 (links could be at the bottom too)
It could be just icons or shorten the words and the search box could just appear when you press the button.
The forum part could certainly use an iPhone specific style that gets rid of the left column and puts names above the posts. Also, since scrolling is an issue, a fixed div on the right that has links to anchors for each post so you can jump through each post in a page quickly and perhaps have the first 3 or 4 characters of the poster name so that you can see the conversation order. Like this:
Remove/hide signatures to keep the scrolling down, change all embedded images to links. The reply buttons would still be at the bottom of each post to reply to one post, I forgot to put them in. There would also be the text zoom buttons like on the iPhone news site to change the text font size inside the layout to save zooming and scrolling.
If you choose thread tools an printed mode, it's a better layout for the iPhone but has no coloring. The square buttons in the image would probably be better as vertical tabs and write the names using css rotation.