I have found that the top of the handlebars need to be above the top of the saddle. For the neck and shoulder pain, I try to squeeze my shoulder blades together every mile or so and look down at the cranks for a couple seconds. You will feel a pulling in the neck muscles but these two movements bring me great relief.
Don't give up - very small changes in handlebar height and reach make a big difference and even a couple day's tour is a wonderful experience. With a few minor adjustments you will soon be there.