I’ve got an online shop plugin (made on my own) which uses custom tables for storing data about products. For list of product and for product detail I created WordPress pages and used shortcode to display list of products and data for a particular product. I use rewrite rules to have SEO friendly URL e.g. /nas-obchodik/chalk-paint-graphite/ will make call to /detail-produktu/?NAME=chalk-paint-graphite. nas-obchodik and detail-produktu are both standard WordPress pages with shortcode. The problem is that Google has never indexed this product detail, even when I try fetch as google and add the result into the index. I found only one article that google index only content return by get_post() method. Is there any solution to add custom table data into google index?

I overrode the default rel_canonical() function and made canonical tag for each product page specific as Milo advised, e.g. <link rel='canonical' href='http://www.navidieku.sk/nas-obchodik/annie-sloan-sablona-antheia/' /> Then I tried fetch as google and add the page to the index but still can’t see it in google search results.

Update 11.6.2015
I tried to use sitemap (XML Sitemap Generator), add few of this pages as an external content. However, google indexed all the pages except of these in the external content list. You can see the list of pages here: http://www.navidieku.sk/sitemap-externals.html
Any help appreciated.