The entire site appears to index fine. As Patrick pointed out, it appears some of the pages in the index aren't https. But I don't know when you made the move, so things may be chugging right along.
The issue is ranking. But I know what you mean.
So what we have is (not all bad, per se - just what I see):
- Previously hacked site
- Timthumb file
- Some very spammy links
- HTTPS implemented on unknown date
- Moved to CDN / WAF
- Redirects
No doubt, you're going to have to disavow the bad links. Take down requests are nice and all, and you should note them in your disavow submission, but you don't have to manually contact each individual link/domain. It's not really a fire-and-forget process. You can submit it more than once.
I would bet a shiny nickle the attack/hack exploited the timthumb file. The site still uses it. Stop using it. Find an alternative. All it does is resize images.
The https migration (redirects... etc.) is just a confounding factor.
After you've removed the timthumb file, request a security review. Also consider the site may still have issues from the hack. So fetch as google from Webmaster Tools. If you see anything different than the real page, you still have a problem.
Read a little more about recovering from a hacked site here. I think that's more than likely the core of the problem right now.