Great start, but.....
I've moved this - because I implore you to make sure you have read all the details you can find about absolutely ensuring that you run the background script, each and every time you load up the gain -
BEFORE you do anything else. Load, click on the Advisor, make sure 1d has been added.
Why are they stuck? (You're not the only one to seem to worry about this.....) Either leave them there a little while whilst you sort out the settlement, rest & recuperate, etc - or - have a Governor ready and waiting, with some occupation troops.
This is something I've never tried and don't recommend. 'Tweaking' can cause all sorts of issues unless you know of every single place in the text files that will be affected.
Terribly gamey - why worry? Fight your battles and see what happens. They will progress at a rate commensurate with what you do with them. There really is no 'leveling up'.
The 'survival script' - I argued hard against this, but.......
It's been a while, I'm afraid I'll have to pass and hope that someone else recalls quicker how to disable that - if that's what you're after.