My initial thought is "ads above the fold". It's hard to tell in Archive.org's archive of your old design, but it looks like ad space increased a lot on the new site? You have the block on the left which kind of interferes with the content, as well as the banner ad on the right which is pretty large (but doesn't distract from the content much).
Plus these ads are not just on the homepage, they are on the inner content pages as well.
They way Matt Cutts explained "ads above the fold" - it's not so much you need to cut down the pixel size of ads, but make sure not ALL your pages have too many ads - so only make a %% of pages on your site have ads, and some not.
I would play with how ads are appearing on the site to begin with.
Your issue does not sound like a migration error, because that is usually immediate. This sounds like something Google takes a little longer to process (page layout / design, user metrics, ads etc).