I have three 'Change Location Event' scenes set up to run in order and they run perfectly. However I am wondering about enabling the two NPCs involved before each scene, then disabling them after so that they appear to vanish into thin air after each scene.

How would I do that?

Edit Scene Data. Stick enable or disable code in the Begin and End fragments. They work like any other fragments.

The problem comes in when the scene wont start without them, otherwise you can't take control.

Start by marking them as optional. Make sure you have a sleep action so the scene doesn't just skip ahead. You could also try using http://www.creationkit.com/ForceRefTo_-_ReferenceAliasif you have any weird problems with the aliases dumping the disabled actors out, though that shouldn't happen.

Beyond that, as Matthiwagg said just put the calls in the scene's begin/end fragment. If you have specific issues let us know and we can help more pointedly.

Yes I have to admit I'm having similar issues you can tick the "allow disabled" box and it'll load them as Reference Alias ok but any scripts attached don't seem to fire unless they're Enabled to start with same with packages and I imagine something similar might hold true for scenes.