slow down, bob...your mind has to keep up with your fingers. this is exactly my problem in certain pieces. i don't quite agree with people who say practice fast. i say, as you do, to work sections, put it together, play it all the way through, and then relax and (sowhat) if you make a mistake or two today... they'll be eliminated tommorrow. just make sure you see less and less mistakes. don't let it stop you from the 'whole' of the piece.
i like to think of my pieces now like a motion picture. you have the intro, the theme, and the development - and you can watch it in your 'mind's eye' and add to it more excitement each time (without sacrificing evennes, closeness to the keys with fingers, and too much or little dynamics). if i haven't practiced in a few days, what is really hard for me is control over what i hear in my head and what comes out. it helps to actually have in your head what you want to hear ahead of time. then you can say "yes! that's what i wanted." or," that didn't quite come out." (blurry, uneven, etc.)
i think pianists can learn A LOT from conductors. the more you watch how they #1 study the score #2 highlight what they want to focus on each practice (and when they get to performance it's ingrained - as you said) #3 learn to go with the flow (not stopping) #4 keep refining especially dynamics (even within dynamics)
one of the best pieces of advice i've gotten is 'remember the context.'