Different strokes, but personally I wouldn't start in California unless you are doing the southern tier in the cooler months. If you must be in California, I'd take the train to Oregon to start your tour. I probably wouldn't shoot for Boston either. My opinion is that the Trans America route does about as good of a job as is possible of sampling what the US has to offer. If I had it to do over I'd do the TA again. If starting early in the season I'd start in the east and if starting mid june or later I'd start in the west.
On shortcutting the AC routes. We did alternates in a few places, but I wouldn't really recommend planning a bunch of shortcuts. Take them by whim once in a while if you want, that is what I have done and it was fun change of pace.
The AC routes are really pretty well thought out for the most part and simplify things greatly. Unless you really want to plan your own route they are the way to go in my opinion.
As far as the mirror... I'd say use one of you do at home, but there is nothing about a long tour that makes it more useful. I do not use a mirror myself and on the rural roads of the west, the plains, and the Appalachians it seemed like it would be even less useful than around town at home.