When you say "clean up" do you mean removing the links or disavowing them?
You will never be able to get them all removed, so in the end you will need to a Disavow anyways. If your time frame is short, you may want to make Priority One be doing a Disavow for each of the 50+ sites you are working with. Then you can proceed with attempting to get the links removed. I have not heard that there is any downside to having a link removed that already appears on your disavow file...
As for the order of the Priorities, you may want to shuffle them a bit depending on the different situations on the different websites. I suggest you read this Moz Blog article called It's Penguin-Hunting Season: How to Be the Predator and Not the Prey
...and then test a few of your sub-pages that used to rank well at the program used in this article which is called the Penguin Analysis Tool. I say sub-page because it needs a single keyword phrase you want rank that particular page for so it do the anchor text analysis. And that works better on focused sub-pages than on general homepages. $10 per website will let you fully evaluate two typical pages on each and see which facet of the link profile is most valuable to attack first.