Over all, using larger AdSense ads, high on the page, usually increases revenue. This is especially true if the page is simple and uncluttered. So if you're re-designing a site, keep that in mind.
Because what you're doing isn't working well, you should feel free to try radical changes.
Have another look at Google's AdSense heat map...
http://adsense.google.com/support/bin/a ... swer=17954
...and study their advice. They know better than anyone what works best, and they're eager to help you succeed because more clicks mean more revenue for Google.
You're already placing ads in good, strong positions.
As you obviously know, from an advertising point of view, the top left is a wonderful spot to place an ad, because that's where our eyes naturally go when we visit a page.
However, it's also a wonderful spot to put a site's navigation bar, for exactly same reason.
Google advises us to "put your readers first" and I reckon that's excellent advice.
If I've successfully persuaded you to make it a top priority to revamp your site to make it more attractive to your readers, here's what I reckon you should do...
It's a bit of a risk, but I'd place a nav bar in the top left, a strong ad for your ebooks top right (another powerful position), and make the articles wrap around a prominent AdSense ad high on the page.
If you had 3 columns, I'd say experiment with an AdSense ad in the right-hand column, as high as you can get it (probably under your promo for one of your ebooks).
That leaves you with one AdSense ad still to be placed. Top of page is supposed to be a good position, so you could simply leave it there, but click the option to accept image ads and test whether that improves revenue.
After you've revamped your site, you could test 3 positions: horizontal near top of page; vertical under your new left-hand nav bar; or at the bottom of each article.
On the home page, where you want to make a good first impression, I'd remove most of the ads and affiliate links, simplifying the page, and making promos for your articles much more prominent, to tease visitors into your site and get them engaged.
One strong advantage of simplifying a page is that doing so makes the AdSense ads stand out. Here's an example of a very simple page with very prominent ads...
(By the way, I think the font is too small, too hard to read, on that page. Some affiliates do that deliberately so that readers give up reading and click on an ad. They may also give up, leave the site in disgust and never return.)
If you don't know about them, I strongly recommend you look into server side includes. They make it much easier to quickly change and test all sorts of things across a site. You can use them for blocks of text, AdSense ads, ebook promos, and nav bars.
For example, you could paste a small bit of simple code into the spot where you want your nav bar to go. Then when you want to add a link to your nav bar, instead of changing HTML and text on 200 pages, you just change ONE file and that makes all the pages change. Lovely! And surprisingly easy to do.