Wordpress with Pestashop store

I just finished designing my website and now thinking I may have done it backwards, but before I change it I am hoping to get some good feedback to make sure I am on the right path before I go through all the work again.

I have a Prestashop store with about 500 products in it as my home page on the root folder of the domain.

I then installed wordpress on the sub domain - /blog and using it to post articles/blogs/info and installed BuddyPress for a community.

Now I thought this was a good setup until I realized that Prestashop uses Javascript and has super long code versus the clean CSS style that wordpress uses.

My question is: Should I move Wordpress to my root domain folder and install prestashop to a subdomain folder such as ......com/store/(product)

Would that give me better SEO in the long run? Or is this not a big enough factor to justify the extra work and worrying about it? Is Javascript that big of a problem in regards to SEO?

I am more concerned with me products having good SEO thats why I originally installed the two programs as I did..figuring products would get better results not being on a sub domain, but I didnt think of the code factor?

Thanks for any help guys!