Thanks for everyone's advice. Unfortunately I only have access to Webmaster Tools and not the Analytics so can't see the previous history.
What I would be worried about is starting marketing the site and then even if it isn't under a penalty now (which I don't think it is), we could walk into one on the next Penguin update.
Should I disavow any link that I don't want to be associated with and explain to Google the situation?
Is it fair to say that if the domain ranks for it's brand name then it isn't under a penalty?
Thanks
James