Magento – Add Shipping Methods for Multiple Stores with Single Website

I think this is the basic functionality of a Magento multi-store, right?

http://www.magentocommerce.com/knowledge-base/entry/overview-how-multiple-websites-stores-work/

You can make domain.com your default store's homepage and then just have two sub-stores with individual CMS pages as your /store1 and /store2

I assume you don't even have the multi-store set up, so I suggest watching those two videos and configuring that locally first.

To start of, this is not possible on storeview level, only on website level. And all extensions I know that can do this work also on website level. I've never tried to get this to work on storeview level but I guess there's a reason why all extensions work on website level.

So, if you can change your shops architecture to website levelmost of this stuff you should be able to do with the free Webshopapps Matrixrate extension. It allows you to set up rules similar like table rates shipping but way more advanced.

If, for some reason, it does not provide all functionalities you need you can upgrade to the paid version of that extension. That one can do literally anything when it comes to shipping rules.