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Fortunately all the afflicted url's seem to be suffering from the same penalty so I would like to a/b test different tweaks and changes (editing navigation, content, inbound links, etc).
My question is how long after a change is made should I wait to assume the test succeeded or failed?
One of my older sites received a google penality for "cough" log spamming..
I was busted when I applied to Adsense.
The site is now well [ unsolicited ] linked from social networks, and some high level blogs.
The site is still in the pooper and I really don't expect to see it ever come back in google search.
Some old versions of the homepage exist in various forms in google search, without a description and will rank on page one for relatively competitive terms, otherwise it is awol.
I could do a reinclusion, but it gets enough profitable traffic without google search, so I am not going to bother.
So some penalities are never removed unless you ask for forgiveness.
Also, the penality goes beyond the domain name, it extends to the content.