yes, stretching will help with your reach and aches, dont be afraid too to make micro adjustments here and there to the bike to fit you. to be fair you bought the smallest size they have so i would assume mekk think its ok for short guys.
but everyones own geometry is different so you could for example have a proportionately longer torso and arms even if your legs are short...
as has been said, simply try pushing the saddle forward, assuming your not massivly heavy you can push it slightly past the max extent that will be marked on the saddle rail, a mate at work by contrast who is pretty short has his saddle pushed all the way back to flatten his ride position. he does 200 milers so i wouldnt say its a pro