Thanks guys for this post,
I am in the same situation, e-commerce site, thousands of products to optimize for, all the tools set up and lots of confusion in my head.
I am optimizing product pages by targeting one root keywords and one key-phrase in order to get low converting traffic and some more relevant traffic. And I am using the on-page moz tool to help me with that.
According to moz I should be shortening all the title tags and meta description which are way too long as well as increasing the relevance of the pages related to the keywords I am targeting them for.
I am doing social as well but Facebook isn't the best social media platform for my industry so I am focusing on Twitter mostly.
Content wise I am writing seo-friendly product descriptions, easy to scan and with relevant information and I am trying to put a content section (blog, news, etc) on the site which hasn't been done before.
Link building is a huge work to do on e-commerce and my thought is to build links at intermediate level, such as category and subcategory pages in order to pass juice to inner pages.
It's a lot of work to do on e-commerce sites and my biggest problem is create a schedule and prioritize things.