All the folks suggestions are on track and are things I've experimented with to help with similar issues. From my experience, you can greatly improve the ride experience by getting measured by a good LBS to make sure you're in the right position. Reach, saddle height, handlebar widths are all things that can contribute to discomfort. I've spent a lot of time and money experimenting and I probably could have helped myself if I'd gotten measured sooner.

One of the things that I can recommend is doing sets of what I call "ergos" while riding. Try to touch the side of your head with each shoulder (leaning your head sideways). Tilt your head backwards and forwards. The one that helps me the most is pulling your shoulders back so your back is straight (I'm rounded over when I ride), then pull your head/chin back as far as you can. (Ooops-just did it and felt my neck "pop"-feels so much better now!)

Another thing I do to help the shoulders (per my orthopedists) is to swing the arms around-move in every motion you can think of. Also take you thumbs and try and reach as far up your spine as you can. The idea is to avoid keeping yourself in any position for long a period of time.

I ride in a very agressive position-the handelbars 4 inches below the saddle-and have gotten to where I do not have any neck pain anymore. I started at a neutral position and over 3-4 years am now at this position and able to do 100 miles rides with no soreness, fatigue, etc.

Another thought is I've have friends switch to carbon handlebars/stems and it helped them immensely with aches and pains.

Good luck!