Im new to this but what I have found out is GREAT!! Good Job. I do have a question though...

I can create slave sites, but I don't want all the components installed on them as they are on the Master Site. How do I remove certain components from the slave sites and have THAT slave site replicate?

Screen shots would be extremely helpful

When you create a fresh slave site, normally you don't have any extension pre-installed.
See the tutorial video CP-04 that is a sample.
www.jms2win.com/tutorial#jms12x-CP-04

If you replicate a website that already contain several extension pre-installed, you can either un-install them from the back-end of the slave site OR use the JMS tools menu to un-install the components/modules/plugins that you want. With JMS tools you can also propagate the action to other children websites.