Yeah, same old story. My first play through I got caught up in adding settlements via the Minutemen. Of course all the nuisance poop associated with kidnapping, defend this, go there gets in the way of enjoying the game. I can't even get the time to hit other quests or build up a settlement the way I want.
I want to add settlements at my pace. Say build a beacon at sanctuary and hand pick a few other places with out beacons and staff them from my ant farm at sanctuary. That way I can build and add settlements and do quests or quest lines with minimal interference.
Also is it possible to add the places I settled into the minuteman fold if I choose to at a later time?

As far as I know all of them. As long as you clear the area of mobs or talk to a named NPC and do what ever it is they need done you should be able to then touch the workbench and then send provisioners to connect you up to your other Settlements.

EDIT ADDED: I know that at least half my Settlements in my first pass I just came across while exploring, I added them to my Settlement network without any problems.

I've gotten a few of those annoying new settlement missions from Preston, and immediately had the mission title pop up 'completed' and reward me with XP because I'd apparently already been there and done it.

All of them, matter fact you can bypass Concord all together and never talk to Preston and his Merry Gang. I have done this with one of my PC's.

Preston refused to ever give me the mission to help County Crossing. Went the entire game with him practically fetishizing Tenpines Bluff and Abernathy Farm. Turns out: you have the option to just wipe out the existing settlers to claim their home as your own. Embrace your Manifest Destiny, Thorrfin: those existing settlers clearly weren't using their land, giving you casus belli to pioneer it.

Maybe I'm remembering it wrong, but I thought that without the minute men, the only settlements you can build on are ones where nobody is living. I think the ones with settlers like Abernathy farm need to join the minute men before you can build. Ones like Jamaica Plains, Spectacle Island, etc...are fair game.

Seems like you can get all of them.. Probably are time dependent or something. Some you might have to make a return trip to get the settlement quest. The only one I can really remember getting a quest from Preston after I had been to the settlement is The Slog. Most of them I simply got the quest from the settlers themselves.

All of them except owned farms, than you need the minute men.

I had some of the owned ones give me their quests without the MM asking me to first. Now I was part of the MM at the time so I don't know if that makes a difference.

Nope, I have tenpines, abernathy, grey garden and a few more I can't remember the names of without being part of the minutemen. If you wander up they will usually give you the same mission you would get as part of the minutemen, they have a different dialogue that say you are their friend rather than "We have agreed to support the minutemen"

When you go to a settlement that you can be sent to by the Minuteman, the quest to help the settlers will happen anyway and you can ally with them. There is no need to even ever go to meet Preston at all.

Weird, maybe my game is glitched? When I got the locket or whatever it was for Mr. Abernathy on my second character (who didn't join the MM) I thought I would be able to build there but it just said "this settlement is not alligned with the Minute Men" or something along those lines. o.o

Probably "you are not allied with this settlement" Talk to him and the wife again and see if it triggers. Theoretically you can just kill them all and take over the settlement that way.