Any question answered...

Question regarding hood position-

At the moment I've got Cinelli Vai bars and R200 brakes. I would like the tops of the hoods to be in line with the bars ala my geared bike but the minute I have this position set up it becomes hard to use the brakes when on the drops.

Is this normal, am I doing something completely wrong?

Its difficult to get non compact bars to have flat top transition to drop levers sometimes. I always found that I had to compromise in one area to gain comfort in another. This page is worth looking:

http://ruedatropical.com/2009/03/road-drop-bar-geometry/