born2run - I know you've been asking questions on the forum over the past two years, but have you been reading anything over that time? I believe this is where it was left.... Not Provided - Looks like organic keyword data is gone Sept-Oct, 2013 https://www.webmasterworld.com/google/4612072.htm
All Google searches, logged in or not, appear to be routed to https today. Clients who previously were running about 40 to 50% not provided are now up above 95%. Looks like organic keyword data is gone.
There's essentially no query info in your logs including query information in the url, which is why you can't find it.
Since the time of the Great Vacuum, SpyFu and SEMrush have been the main tools available for keyword popularity, both PPC and organic, but that's not the same as referral information. I've also been frustrated by lack of information on keyword phrases that aren't the most popular. Both tools have an incredible amount of data, if you can apply it to your situation, but IMO they're not good in long tail.
For matching referrers to landing pages, there have been several suggestions for ways of combining WMT and Google Analytics data... You spot poorly performing urls in Analytics and and match them statistically with likely queries noted in WMT, using Excel and regular expressions, and several other tools. How To Replace Google’s (Not Provided) Data To Strike SEO Gold Chris Liversidge on May 5, 2015
The key to matching these data sets is a firm statistical bond — our zipper — matching the keyphrase to the landing page.
I haven't heard of third party reports from those that have tried this. Would love more feedback.
Shai, it would be helpful to know more about what clicky does that GA doesn't. Is the free version at all useful? The site seems to want you to sign up before they get down to the nitty gritty of what the software does, and that always bothers me. I'm assuming if you recommend it that it has some good qualities. What specifics might be useful in this situation.
I have my own theories that it's better to target your demographic and various likely uses of your products than it is to chase keywords. I'd particularly avoid chasing subtle long tail variations via multiple pages, which might even be seen as doorway pages.
But it's good to do some basic research for core terms that have proven historically popular. Unfortunately, we've just lost the auto-suggest data that we had in our WebmasterWorld free tools... Google shut down the API to everyone earlier in the month.