Appreciate the work and feedback. I am on PC now (working on new forum name) but have moved on to a new play through. Can I just zip and post the save file to the forum? I don't have a google drive or other such account. One thing that might be relevant is I think I may have done all the power upgrades while waiting for Perception settler so get trained up so the Commonwealth Rising quest had not yet progresses past "Recruit and assign staff to Engineering..." My plan this time is to staff up Engineering before moving on the HQ power upgrades.Sorry you are having so much trouble with this - it sounds like you have everything setup correctly. If you were on PC, I'd ask to look at your save. Unfortunately there's no way I can make any meaningful change to resolve this for you without being able to replicate it.
This may be a bug that's difficult to replicate. Whether bug or not, it is a problem that you spent all of this time grinding in the dark trying to fix it, so a reminder to me of how important it is to give you guys plenty of information in-game about the state of things (ie. reports). Working on it actively - we are trying to get an in-game map going to show data about SS2 connections, and I'm creating some new reporting tools for the next patch.