I want to be able to set my target disk and reboot in windows remotely, can this be done?
I have SSH set up and am able to log in from outside of my network.
If I understand correctly, I don't see why not. Does each "target disk" have an entry in the GRUB menu? If so, there are a number of strategies you could use. If you are content with having a default boot option, you could simply edit the file /boot/grub/grub.cfg to change the line
This file says "DO NOT EDIT THIS FILE" at the top, but that is only because it gets regenerated, and will reset to the default when this happens, either during an update, or when you do an update grub command explicitly.
This can easily be scripted if you don't want to edit the file. The easiest way is to use sed, which can find and replace that line in the grub config file.