Man what a difference those last changes made!
I'm super stoked about it now. Being more upright, for me, is absolutely the right choice. Being able to see all around without straining is so nice. The mirror may have paid the most dividends. I definitely was able to reduce the number of close passes by seeing cars coming and positioning myself to eliminate that possibility. I feel much more in control and in turn safer by being able to see behind me without doing a head check constantly.
The bike fit is getting very close now I think. There seems to be a balance of the weight distribution between my hands, butt and feet now. I think I may need to adjust the angle of the saddle a little but other than that it feels very good.
My average speed seemed to be on pace with my other morning commutes so I don't feel the riding position or the panniers provide any hindrance to the speed of my commute.
I'm happy!