I have two blogs, http://www.architecture-student.com/ and http://www.civilprojectsonline.com/ I was experimenting with adsense placement. I have doubled my CTR. The results have been consistent for the last 7 days now. My CTR jumped from <2% to 5%. All I did was to shift my sidebar from Right to Left side of the content. I am glad I did it. My blogs don't look as good as they used to, but I am getting a lot more clicks and income. Its a trade-off. Cheers!
I found that excellent free theme "Fusion" which is highly customizable. I don't know how anyone can just give away something so good for free. Its very hard work. I have modified it a bit, and can tell you that coding is clean and of high quality.
Nice work. I used to move or shift from one side to another. Sometimes it seems like moving them around helps for a while then it's like they get used to where they are or something. Maybe regular visitors. Move them around and they pick up slightly. You never really know though. Hope it continues to work out for you.
Show less posts per page and I think your ctr will further increase. BTW these themes are known to get upto 8% ctr.