Hi there,
These are my own personal opinions based on a significant experience using AdSense on a wide range of blogs, message boards and websites. They may or may not work for you.
1) In my experience the best performing AdSense formats are 336x280, 300x250 and 728x90 to a lesser extent. Although ultimately your earnings will depend on CTR (clickthrough rate on your ads), advertisers in general are slowly moving away from formats like 468x60, 234x60 and even 160x600. This means that you might have a smaller advertiser pool for those formats, so I would keep away from these formats and bet on those formats that are likely to have more ad variety.
2) I would make your site wider to take advantage of the real-estate in modern screen resolutions. This would also allow you to (i) make the right-hand column wider in order to fit a 336x280 AdSense at the very top of the column where you currently have the PDFbiz logo (ii) include a 728x90 in the body which will probably work better that your 160x600 and (iii) add a fancy header taking up the entire width of your website directly above the navbar.
3) A fancy header is good because it will attract the attention of the User, especially if you have a nice header graphic which is deinitely missing on your site. I typically create a two-cell HTML table for my header: the left cell includes a 300x250 AdSense unit and the right cell (much wider) includes the actual graphic with site title etc...
4) Finally, I would include a 728x90 between the second and third posts of the home page. If you want to risk it, you could insert it between first and second posts, but after Google's "Top Heavy" algorithm update I would only want to have two AdSense modules visible in first screenshot.
5.) Regarding interior post pages, according to my model you would already have a 300x250 on the header, a 336x280 on the right-hand column, so only space for one more ad (excluding Link Units). I would go for a centered 728x90 after first 2 or 3 paragraphs.
6.) Oh, and I would leave only one search box. No need for two.
I have created a mock-up for you:
View attachment 25483