Let's wrap it up!
Okay I figured I would wrap this up as I really never expected a real answer, especially with all the Bethesda scripts and hundreds of unknown mods trying to run at once.
Basically I restarted a new playthrough and this time I manually built Sanctuary, Red Rocket, and Abernathy, and didn't touch anything else. I kept the settlements basically as small as possible while having enough materials to have stuff to build the HQ when I got to it. I focused entirely on the SS2 questlines except when I had scripted downtime, and then I did some minor exploring and questing.
I have to say that having settlements unlocked, but NOT inhabited really made it easier during the Gunner attacks, I think it gave me a buffer, sure Sactuary, Red Rocket and Abernathy where being attacked on a regular basis but I had an hour or two before attacks instead of the nomal 20 minutes. And all my other settlements have qued up attacks that I just ignore.
Happy to say that everything worked as advertised and Aiden did not follow me except when he was supposed to. I did however run into the bug where the HQ is under staffed during the tutorial, preventing you from completing it. Luckily I found the answer here on the forums, and used the advanced tools on the Holo Tape to fix this apparently known issue.
So off I go, to begin building my empire anew!
Thanks everyone for thier input.