Questions about additional stores

I have a few questions about creating additional stores. Are the additional stores completely independent of the main store? Can a different default email be setup for each additional store? Can different shipping charges be uploaded for each store? One final question for now, is there a limit on the number of additional stores we create?

Stores are "almost" independent.
Essentially, they're different skins to which you can assign products which are already part of your main store.
There are some variables you can configure, but that's only what you can see in the stores setup. Mainly, you can change the look and the final "thank you page", often used to process payments in case of integrations.

But still, they're sub-layouts of your main RTD account. So no, you cannot have multiple email addresses or separate shipping charges. This is also to protect ourselves, otherwise technically you oculd use only one RTD account to run even completely separate bizs!

And to reply the final one no, there's no limit to the number of stores you can create.