This may not be what you want to hear but this is something I've tried myself and it didn't have the desired effect.
I have a thread sharing the process I went through here - [webmasterworld.com...]
Essentially, as confirmed by Google's John Mueller, Google still treats the website as a whole algorithmically. Obviously the links pointing to one version or the other (and setting preferred version in WMT) helps a bit but there are still overriding associations which you can't shed.
What happened to me is that I was caught up in this associative part of the algorithm. Some time afterwards I was given a manual penalty for exactly the same reason despite me having no unnatural links pointing to the non-www version of the site. I ended up getting a new domain in the end (different TLD) and haven't looked back.