Thank you all for the excellent help! I did 16 missions for the same agent and then got an email offering a storyline mission. I guess I must have missed several of these! I saw several expired offers in my inbox!
I feel like such a fool.
As for “The Plan” it is an excellent resource and I learned a lot about factions, standings, and all the ways to fix whatever ails you. It’s exhaustive and plumbs the depths of faction mechanics in a way I was not able to find in other sources. But it is still very complex!
Oh yeah. I didn’t know that one could decline missions and the agent would turn right around and offer you another one! I thought you had to accept and complete a mission before getting another one. Now, when I see a mission that might cause issues with the main factions, I decline them.
This one tip will save me much crying. Thank you all.