Q1) In JMS, you can give several domain in the definition.
you just have to give several domain based on your sample
www.{site_prefix}.{site_url)
{site_prefix}.{site_url)
{site_url} contain the current URL and therefore the URL used to access your master website.
If you want to be sure, you can hardcode your master domain name.
put something like {site_prefix}.domain.com
Q2) All depend if you have a full access to your server and if you have the possibilty to configure your CPanel dynamically.
You could develop a specific interface to your hosting server.
As this is specific to each hosting provider, JMS just provide the possibility to execute additional script.
See user manual chapter 4.2 page 35 to 45 that describe all the possibilities
If you want that we help you in this development, this is possible with billable support.
We could work with you to develop such interface for your system.
Billable support can be ordered on
www.jms2win.com/download?page=shop.produ...35&category_id=1
Q3) The current JMS 1.1.x does not allow to create slave site into another DB.
I am working on JMS 1.2.x that will allow replicate website into another DB.
It will have some constrain like having enough MySQL permission to create the DB and users.
I hope it will be released in june or july.