This is slightly tangential, but we did a project for a client in a similar field to you and concluded that duplicating products for each school would create a data structure that would be increasingly difficult to maintain as they grew. So instead we had them identify their actual products i.e. sweatshirt, T-shirt, trousers, etc. Then created a category for each school and linked the products available to each school to their category (we automated much of this and provided filters for color attributes so that only the schools colors showed up in the school's category.
I don't think we went so far as to automatically take a customer to their school's shop when they logged in. But with the above data structure, that would be a simple matter of going from the login to the index listing for the relevant category - though complicated a little if a customer has children at different schools.
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