Assuming that your bike is the correct size, and the the saddle is level, and at the correct height, pain in the neck, crotch, wrists or hands is caused by having the bars too low. The correct height for the bars is with the highest part of the bars (next to the stem) about level with the highest part of the saddle.

Pro cyclist keep their bars lower, because at 35 mph, a lower position is slightly faster. They get a neck and back massage at the end of the afternoon, and a fat paycheck to endure the pain. You are not getting paid to ride, and you are unlikely to get a neck massage after you ride. Raise your bars.