Carl, I have a few ideas and suggestions. I will respond to your original mentions:
"Obviously, the affiliate store will not be unique content, it will be made using the datafeeds from cj.com et al, and so I don't want to get any duplicate content type penalties from Google for this store."
I find this interesting that you automatically assume that you have to use the original datafeeds from CJ. I would encourage you to contact Commission Junction directly on this matter. Many services allow you to provide an alternative product description, etc.
The faq section of feedwizards has an example which you can read about here: https://dashboard.feedwizards.com/faq/9 (look for: How do I avoid duplicate content on shopping engines & affiliates using my feeds)
Matt Cutts as also spoken on this topic as well in the video I included. http://www.youtube.com/watch?v=z07IfCtYbLw
Hope this helps 
