tedster - 3:07 pm on May 18, 2013 (gmt 0)
Sorry that we can't assess how your site lines up with or violate Google's quality guidelines here, because we don't do public site reviews.
I used the disavow tool to disavow EVERY domain linking to subdomain1.domain.com
That sounds very problematic to me. You have removed ALL traces of PageRank flowing to that subdomain, and without some level of PR it is very difficult to get and significant search traffic.