Hi David,
First, you should use the last beta 02.01.20 with dnn 5.1.2, please read this post.
To create your own version, you should install the source version, please read this post (translate version numbers as needed, the process remaining the same). PLEASE follow my advices, because the Store module is NOT the more simple module to begin with dnn! The VS solution contains 21 projects in C#, I hope you have a strong knowledge about ASP.NET, C# AND the WAP programming model.
a) Yes, you can do it easily.
b) There are several ways to do this. May be the simple way is to modify ProductController.cs inside the DotNetNuke.Store.Catalog project. You will find several functions related to the catalog products like: GetPortalProducts, GetPortalFeaturedProducts, GetCategoryProducts and so on. Each function call the corresponding function in the SqlDataProvider to retrieve a DataReader, then call the standard CBO.FillCollection. This method return an ArrayList of ProductInfo class filled with data from the DataReader. You should parse the collection and call your webservice to retreive the real stock quantity from the second store and update the ProductInfo..StockQuantity property.
Gilles