Guys,
I'll try to get a pick as soon as possible.

I should mention that I am new to road bike, and come from a mountain bike background, so the geometry and positions are new to me...and simply need to work the muscles I've never worked before (lower back, centre of my neck). There is no pain on my shoulders or anywhere else...just the the center of my neck from looking up. When I am in the tops, I am ok. Just the hoods / drops.

I am on a fitted 54CM Trek Madone 5.2 H2 w/ 90mm 7 degree stem (original was 100mm). Stem is angled down of course.

Seat is more "forward" than average, but this was purely for Knee over Pedal and had nothing to do with compensating for reach. My knees have the proper bend in them, and everything is working good except the centre of my neck.

The only thing I do notice myself having to do is move my butt back onto the seat, as opposed to carrying my weight with my hands. Maybe 1-2cm adjustment to get my seat-bones "realigned" with the saddle (which btw fits me great when I am positioned properly)

I am 5'9, 150LB, and pretty flexible (hence the H2).

This could just require me to ride a bit more to get used to the new positioning.

The bike was fit properly (6 pt fit, not machine / BG fit) by a shop that caters to all levels, including racers / advanced riders. The shop had me on the trainer twice and said I looked good when on the bike, my back looked great, they said I looked flexible for the fit that was configured for me, and had no impression that I was "Stretching" or anything.