The ad placement is okay, you might want test out the site in IE because the right menu goes all the way down.. (there's a <td valign="top"> missing in your table)
I would give the link unit, a dark background and white text - to make it appear more menu-like. I owuld also place your square ad unit nearer the top of the left hand column, perhaps under the picture.
Your adsense placement seems ok - Due to bigger images your right Nav bar has slipped down the posts. If you expand Wrapper's width in template it will fix your probelm and your blog wont look (posts only blog and no nav bar) Hope this helps