It new arising after the new fit and only occurs well into a long ride. Correct? If it goes mostly away after getting off the bike and there no significant next-day pain or continuous pain at any level a couple of days after the ride then it is most likely the fit. The fit can be by the books perfectly but you just happen to have a shoulder that doesn't like it. It happens. (Look for an injury or genuine shoulder issue if it still occurs after altering the fit to lessen the weight on hands/shoulder.)