Long story short, there's a site that was penalized and bad links played a big role in it (WP theme footer links - there's a lot on that sad story in my previous posts back in 2012). By a strike of luck most of those bad links are now gone - couple large sites using my themes have closed and some webmasters actually responded to my requests to remove - but a few remain. No reconsideration requests have even been successful, but that was before the disavow tool was created.
I have eventually moved the site in part due to much better brand-ability of the new name and in part in hopes that penalties would not follow. They did.
I am redirecting all pages of the old site to the corresponding pages of the new using 301 with one exception: the google authorization html file. As such, I have both sites still active in my WMT although I have filed the "change of address" for the old site, so I can now see all bad links in the new site's data. But I guess I can still file recon. requests and use disavow tool for either or both sites since they are both still on the list of my sites.
So, here is where I finally get around to my question: what strategy for using the disavow tool would you suggest?
1. use disavow tool on the old site, wait few weeks, file RR for the old site.
2. use disavow tool on the new site, wait few weeks, file RR for the new site
3. use disavow tool on the old site, wait few weeks, file RR for the new site.
Or maybe even something entirely different? Anyone has an actual experience with dealing with this kind of moving site situations?