Seems unusual that you have now started getting aches- even though you have done more milage. Look to see if anything has changed on the Seating or bar position. You have said you have flat bars so a riser bar will help. These will raise the hand positition and bring it back and depending on the "Sweep" can be just a bit or as much as 5 cms. Then there are the Bar ends. they will give you alternative riding position to help ease the one position ride and the aches that will bring.

OR it could be that you need more practice in the longer rides- and the pain will go after a few more rides.