This is what I'm doing and this is the internet so take it as you will:

I've been working on getting lower on my roadbike. Bending arms more, riding longer in the drops. I've had to adjust the nose of the saddle down more and raise it higher as I've done this. Neck and shoulder pain I've reduced sustantially by working on my latissimus muscles to pull my shoulders back. On longer rides I'll catch myself slipping back to the old ways. When I pull my shoulders back I get pretty quick relief of the pain.