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Thanks Patrick, that's really helpful.

I think using the .com would be fine. I would avoid 301 redirecting the penalized site to the clean domain.

Was going to send you a PM Colin but I can't. Drop me a mail over to info@inetseo.co.uk and will give you a tip or two -Andy

Google doesn't believe these links are natural ones because they represent no value for a website visitor. From what I know the advice is to make them nofollow if you still want to keep it in the footer of the websites. Personalty I would go with another solution - I would place a dofollow link on a single page like for example the "About" page if it contains details about the website also and not only the company or on an "Impressum" page if the website has one.

That's up to you. There's no guide that can tell you how many times to contact a Webmaster or how often. Just try with the available means: email (if any), social (if any), phone??. The important thing is to document your process, responses, and actions taken (link removed, wants to charge me to remove it, no response - disavowed, etc). The more you wait from the moment you start your analysis and the moment you request the reconsideration the worse it becomes. Sometimes, Google finds links that they were not part of the previous file you downloaded. Recommendation: once you are done with the assessment, do it again, but really fast and only with the new links (under WMT), then send your disavow (you can wait a few days now), ask for reconsideration. And don't feel bad if Google responds with a negatory with 2 new links that were never listed in previous exports... it happens almost every time.