You didn't mention the year/model...
I'd check if the wire is hot at the trunk servo when the switch is pressed (use a test light or voltmeter) - if so, your servo is probably bad.
If not, I'd pop out the trunk switch and test if one side is normally hot. If so, see if the other side is hot when the button is pressed. If not, use the tester on the fuse terminal to see if it's actually hot.
Btw, if the trunk switch has juice it's probably not related to the window problems.
That should give you a starting point, and you might use a similar tactic on the power windows.