Give it some time ... things will auto correct with the Canonical issue out of the way. Patience is especially important since it all depends on SE crawling, indexing etc.
i have removed canonical tag from all pages of site. How much time it's take to cache internal pages. Today, my home page is cached only 13th December. It's negative sign from google to mine site ? Cache only Home page ?
hey there a good place to start in terms of getting an understand of how the major search providers see your site is http://www.seositecheckup.com/ - it's a free service that gives you a view of how your site is structured and whats good, bad and what needs to be improved. Have a look at that and let me know how that goes for you. Cheers for now. Darren