I'm trying out the new version. I like the new functionality.
I did find a bug. On multi-post pages, the header link is incorrect. It uses blog address/post name, regardless of the permalink scheme the blog is set to use. My test blog has permalinks off, so the link fails completely.
My live blog uses a different permalink structure than what is hard coded in the theme, so I would run into problems if I upgraded. I think the links would work, but the header links would be different than the "Recent Posts" link to the same page. That would create canonical issues with the SE's.
I have another issue that's not related but not really worth a post of its own. I'm not a big fan of the new footer links. I understand the SEO basis for doing it that way, but I think it looks "spammy" and I don't like it on my blog. I am happy to have a link to you, but I don't like the way it is set up now. I'd much prefer you to go back to the old format.
Thanks,
Brad