I have changed the cockpit of my bike recently and did a few of 1 - .5 hour rides. During and after the first couple of rides, my upper shoulders, and neck were sore. Muscle tightness type of sorness, but very stiff and sore around the shoulder blades, between the shoulder blades, the trapezius muscles (neck to shoulder) and my neck. It wasn't debilitating, but very uncomfortable.

Today I did the longest ride of the year, around 2 hours. I felt pretty good during the ride and feel fine now (several hours later). A very significant improvement over yesterday and the day before. What I think helped:

Just putting some time in and getting the muscles tuned up a little.

Concentrating on relaxing my shoulders while riding. I definitely was hunching them and keeping my arms too straight. I constantly reminded myself to relax my shoulders and tricepts muscles, relaxing my arms, slacking them at the elbows. I think this was a huge help, but it takes some thought and time to develop the habit.

Finally, for the past two days, I've been stretching. For me, stretching is the missing link in all my athletic endeavors. I concentrated on shoulders and neck but also did legs and hips. I think this is also very important in my improvement.

Good luck.