Shims work great if needed, once installed brakes are adjusted to be just as responsive.

On bar rotation, whatever your comfortable with is best. I like a flat top, because it lets me ride in the hoods all day long, and I can still do a 30 minute TT in the drops. It will also allow you to ride more aero by grasping the hoods like a gun while resting your forearms on the bar (sort like having aero bars without the aero bars). John Howard really pushes this technique and while I don't use it often, it works well.

I think your on the right track with your fitting. The first fitter I ever had always said start with the ground and work you way up. I've had different fittings over the years, but his approach was very systematic and makes sense. He started with cleats, (he was a Lemond wedge fan as well), then worked up to the saddle/seatpost, next the bar, and finally the stem. And repeat.

I'm getting ready to have Retul fitting done, and look forward to how it compares to past fittings. It uses sensors and a computer to draw a 3D image of what is going on in real time. Should be cool.