The shoulder and neck discomfort are are likely due to lack of fitness or just not being used to the position on the bike. Due to worsening asthma, I've not ridden the bike at all this winter, whereas my normal long ride has been 50 to 60 miles. The result has been some discomfort in a mere 15 miles even after raising the bar somewhat. This aspect of your discomfort will resolve itself in time with increased mileage. However, I'm surprised by the saddle to bar drop being excessive. This indicates the fork was cut too short for you. When new and uncut, the fork is way long and even when cut, is left on the longer side until the new owner settles in on a final position on the bike. I would suggest you ask the shop if a the fork can be swapped out for one that is uncut until a final fit.