I found Fresh Store Builder last year and absolutely love the script. I've been building a site like you describe with both Wordpress and FSB, which you can see over at WiselyOrganic (dot) com. I'm still filling the products out, as I'm re-writing every product description to be unique, but you can see how I integrated the two.
I installed FSB into a /store subdirectory, and put WordPress into the root. I then customized FSB to match my WP
theme. In hindsight, I picked the wrong theme to start with so I had to pull components from the other themes to get what I wanted, but I was able to adjust it so it matched my blog theme the way I wanted.
For me, the choice to put the store in FSB came down to a couple of factors:
1.) The ability to hand-pick the products I want, or the flexibility to take everything in a category node.
2.) The ability to control all the content descriptions, re-write my own, control the MetaData etc.
3.) The ability to shop and put all the items into a Cart, and then check-out all at once and transfer to Amazon.
4.) The coding behind FSB is standard PHP
, with a nice separation of code from presentation so modifying the CSS
I'm eventually going to be creating themes for FSB, as I see it as a very strong tool for Amazon affiliate stores - but the number of templates is limited. The FSB team is working on a template system for version 3 that will allow us developers to create themes for the platform. Once that is released this year, you'll see more themes being created. In the meantime, you'll need to customize yourself or hire someone to help you - but it's completely doable.
If you do look at my site, I'm happy to hear any feedback you might have :-)