yeah dude, primo PDF can be a real pain in the butt. I beleive there is an option to export as ebook with that. Which should help...
I think the problem lies with links that are called something else... like when you say:
CLICK HERE and that links to your site there is a problem...
but if you just put in the URL like " http yourdomain .com " it should show up as a working link.
As well if you own adobe acrobat you can manually add the links in.
If you really can't figure it out I would be willing to fix the ebook for you with my copy of adobe... PM me if your interested
Perhaps you can throw one of my affiliate links in there somewhere as a thanks 
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