Back and arms aching could be just you getting used to things, but an aching neck would suggest to me bad position. Are you straining to look up all the time? If so maybe consider:
– Shorter stem
– Spacers to bring bars up higher
– Rotate bars so the sweep brings them up a little
– Move saddle forwards/down a touch
Are you riding with a heavy pack? Or one that restricts your head movement? If it’s a tall pack (daypack meant for hiking maybe), combined with the extra bulk of a helmet it could be pushing your head forwards too much. If it’s heavy, combined with a bad position, you could be putting extra weight through your shoulders and arms.