Hi,
The confirmation email is controlled directly by the class "order", but you can create a plugin based on the function "onAfterOrderUpdate()" in order to send your custom email, and set the variable "$send_email" to "false".
By this way you can have different emails depending on the payment methods, etc.
That's for the email part.
Regarding the custom fields, you can potentially edit the view "checkout / custom_fields" in order to display or not custom fields based on their name and on the payment method selected which can be found in session.
I think that it's the easiest way of managing your issue, having two different installations can handle a lot of works after, create products trwice, checking the orders at two different places, etc.