Hi Jane,
to clarify, the site had been hit heavily by Panda in 2011 and again in 2012 by Penguin. Both are prior to the manual spam action, so we are aware of the impact each has had.
The purpose of the post was to see if anyone within the community has experienced a similar error in communication from Google and could recommend a course of address.
We are also aware of the backlink profile and manipulated anchors, but would like to thank you for your analysis.
Regarding the miscommunication, we have decided to approach a few individuals from the webspam team on Google + for a resolution.
Thanks again for your input : )
M.