I'm working on a site that has historically had issues ranking the homepage. We cleaned up some on page issues and then it went into a high and low pattern - page 4 then page 12 etc (was static around page 9 before), settling at page 6.
The link profile was not good and there were a high level of links that should have been no-follow as they were clearly looking paid for - we addressed this along with some other poor links. This effectively dropped ranking down to page 23, but not unexpected considering the very big drop in followed links.
Meanwhile we have embarked on a fresh steady link building strategy with nice clean links, varied anchor text coming from varying DA domains, smattered with a few no-follow links - strongly focussing on being as natural as possible.
At the Penguin update the homepage has totally disappeared. Frustratingly just after the update (same day) we removed a 301ed old domain from the profile. This was the old company URL which we discovered had a lot of spam linking associated with it. An oversight - there were other 301 domains that were removed some time ago which were totally unrelated to the main site and we were told all other domains were simply bought and redirected to stop hijacking - all but this were.
Considering the work we have done would it be good assumption this domain 301 could be the underlying factor? So far organic traffic is steady, in fact a tad up. What would you guys do?