You should check out majestic. With Majectic -- to get the most out of their free account, simply add the meta tag to your site and then confirm it from within Majestic and Majectic will allow you to run full link analysis on your site(s). This will give you a huge list of most all of your links.
Ahrefs will provide the same. You need to signup for an account on either of these platforms. Ahrefs will allow you 3 reports free with your account.
I would recommend that you get a fill link report from these two places and implement them with a compilation of GWT as well as these other 2. This should make a nice list for you to analyze with link detox through link research tools (LRT).
As mentioned earlier, you might need to disavow all of your links. Although some may have passed link juice, how is the anchors? Are they spammy?
Once a link has been established for a long while, I (in my opinion) don't believe it's very beneficial anymore. Meaning: if the link has been on a spam site for a long time, you've gotten just about all the link juice you're going to get from that.
After you run a full analysis, you not only need to check the links, but check the anchors and other metrice to determine which links you want to keep.