I'm laboring under the apprehension that you mean the site you listed in your profile. If that is the case, based upon what I've seen - the site isn't as mobile-friendly as it could be. I would recommend looking into responsive design.

What has likely happened is your content was pretty good for queries on mobile devices, up until recently. Competitors are likely serving up content that's 'mobile-friendlier' than yours in some way. That could mean anything from faster page load speeds to actual dedicated adaptive or responsive sites have started crowding the SERPs.

However, there are more pressing concerns that can be remedied now. The www and non-www version of the site is thoroughly indexed. If there's been a change to the .htaccess file, it would be a good idea to revisit it - the sooner the better.

Also, my crawler is picking up some 500 errors in the tag and category folders. Finally, it appears there is some weirdness happening with the /log-out page. It would be best to noindex/nofollow that page and/or block it with robots.txt. It appears to be sapping crawl budget.

So I suppose:

1. Look into the duplicate content issue.
2. Fix crawlability issues.

If you would like, I can share a Google Sheets copy of the crawl - free of charge. Just message me from my profile. Hopefully this has been helpful.

The difference between the number of links you see across various sources is because of the resources themselves. Some backlink services only crawl so much. Google can only crawl so much of the internet.

Your best bet is to use multiple sources. I would go with GWT, Majestic SEO and aHrefs, then filter duplicates. You'll have a much better understanding of where the site stands. Once you have that, you can use Cemper Link Detox to upload the data.

Be very careful, Link Detox still throws some false positives. Though I expect it to get better every day. There's a machine learning element to it that's based on human feedback.

Finally, I would be very careful of fully automating anything like a disavow/removal process. Do you really want something so delicate taken out of your hands? It's still very necessary to manually check each link so you know that you're getting rid of the bad and keeping the good.

Link Detox is the closest thing there is, that I'm aware of, that will help 'automate' the process in a safe-ish way. The subject of link removal/disavow is something so sensitive I wouldn't outsource it. Then again, I hate the idea of outsourcing overflow blog writing work to competent people. Call me a control freak.

This sounds like it might just do the trick. You'll need to have Ruby installed for it to work. If you have a Mac, it's already on there. If you have a Windows you'll need this. It's pretty easy, I installed Ruby on my Windows gaming rig. If you're running a Linux flavor, try this.

Just take your URLs from the site crawl and make a txt file. You can compare that with your CSS file. I've never tried it on a large site, let me know how it goes for you.

I would run them through Copyscape to check for plagiarism/duplicate content issues. After that, I would check for referral traffic. If there are some pages that draw enough traffic, you might not want to remove them. Finally, round it off with a page level link audit. Majestic can give you a pretty good idea of where they stand.

The pages that don't make the cut should be set to throw 410 status codes. If you still don't like the content on pages with good links and/or referral traffic, 301 those to better content on the same subject.