Looking great Boochman!!
I did notice.
It seems like your flack jacket shoulders come down quite a bit more than the reference photo. I think this is why you are having problems with the shoulder armor alignment.
My shoulder armor is not perfectly lined up either, but the 501st didn't point this out and I never noticed.
Before you have any alterations done to the flack vest make sure you suit up with your jet pack harness.
Mine makes a big difference in the way it fits. I have the Big Dane scuba harness which is a little bulky under the flack vest.