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Sorry, I'm completely confused - you said that there's no notice of a manual action in Google Webmaster Tools, but the manual action page isn't empty and Google is giving you examples of URLs? If the page isn't empty, then you have a notice of manual action. I think I'm missing something. Did the message come and go in GWT?

Hi, thanks for the hint, we added bot the canonical url and the category page. cheers

I don't think it's a problem providing all the links on your site are up to date with the new URLs and the sitemap.xml's are also up to date. Google will respider and reindex your site with the new URLs and drop the old ones. You only need to keep the pages which have external links pointing to them 301ing. All other should just get reindexed and Google won't report hundreds of thousands of 301's if the URLs in your code are all up to date. You don't want your site to have a navigational structure that consists of 301's, and you definitely don't want to daisy chain 301's.