We made years ago a tool for your users to count pregnancy dates. They user to copy a small code and paste into their own sites to show their pregnancy due dates. This is since many years the case, how ever we did not take care for the links in this counters and they all point back to us with rel=nofollow. We did implement this later but there are thousands of these old links in mostly abandoned blogs and forums.
To get rid of these inbound links from this pages we tried to contact many many users but did not get response form more than 5-10.
We could not disavow with the google webmaster tools the entire domains but the problem is that not all links are bad in these domains. For exmaple from blogger.com we get like 500 links to differant urls (articles) which are good links but we get on the other hand thousends bad links for the counter.
questions and ideas
1. Could we even use the disavow tool to disavow approx. 90.000 links (single links)
2. What if we block via robots.txt the url which this inbound links jump to and their for tell google that these links are not to be used. If google indexer can't reach and index the jumped url should be also nout counted as bad inbound link since now SEO value is behind as well.
3. What if we just outsource the entire counter system to another domain (or subdomain) and redirect all inbound links to this counter via 301 (permanent to the new domain) in normal conditions this should count all for the new url and not for the old and their for not be negative for the old domain. We could even use a 302 which dont forward any SEO value as well.
I appreciate your comments and input,