Welcome to the Q&A Forum

Google bot definitely won't ding you for duplicate content based upon you sidebar, header, and footer links. I've managed several ecommerce sites and have never had this problem. However, it may still ding you for duplicate content if you have several matching pages with you main column being the same.

Yes, definitely add some unique content to these pages to reduce the levels of duplicate content which you're currently experiencing.  Hate to state the obvious, but be sure to avoid using any manufacturers standard descriptions as you can guarantee that they'll have been repeated on other sites who sell the products. Your own unique product descriptions and also something which states that the product is not currently available, with some alternative suggestions perhaps may well help to deal with any negative user experience.