Can you get rid of a "foot print?"
 

One of my main sites that has good SERP... I have another site I did (several years ago) that uses almost identical html code. I basically cloned them, I guess. They also use the same registrar and both are on the same host (hostgator).

This second site... could I move it to another host and transfer it to another registrar and also change the html code and then have it benefit from SEO techniques going forward? Or is it doomed to be penalized forever? BTW, it has decent SERP, so, I don't even know if it has been penalized by Google.