Thanks for getting in touch with the Community.
So of your 3 questions I'm going to start with number 3. (Too many people start at number 1, lets be different!). You mentioned specifically in this point that you were changing the email template, unfortunately this is one of the few things that can't be set to be different for each invoice template. I know this may seem unusual as there is still the option to change the email when editing the template but the email that is sent out with the invoice will take effect on all invoices.
Regarding points 1 and 2, would I just be able to confirm if you are changing the master template on the Custom Form Style page or whether you are changing one of the created templates. I also just want to check if the templates to which you have made the desired changes have been selected on the invoice page itself when creating the invoice. If you click on the Customise button at the bottom of the invoice page you will have the option to switch between the different invoice templates.
Let me know and I will be back in touch