That's actually pretty easy to do. I use the coastal Cottage as my starting point. I make sure that they are the only one living there, I gear them out how I want and then when the time comes, I spawn something to attack...usually a deathclaw on the second story cuz usually it gets trapped. The settler will fight for a second but then they notice a nice new suit of PA and jump in. Once the fight is over I simply send them to where they will be living permanently and off they go. It gets a little tricky after that depending on where you send them. Some places have a bunch of built in idle locations or something...where they stand next to a wall, or try to fix the place up and to do that they leave their PA. So you either have to assign them quick once they get there on their own, or I use the Moveto Player command and that makes it a lot easier. Provisioners are easy, but Guards seem to more or less stand in the middle of the settlement most of the time. But they react just as good if something comes in range of the guard posts...so...<shrugs> I did have a thought about replacing the damaged pieces but haven't tested it yet. I thought it might be possible to pick pocket the broken pieces, repair them, and then reverse pick pocket them back...but I don't know if they would re-equip them or not... But that is a HUGE hassle once you get a decent number of supply lines going.