I'm with Velogirl too, I think that its your body getting used to the new demands.

I remember my hands used to ache after every ride, because at the start of leaving there is alot of downhill (600' to sealevel) and I used the brakes alot.
It took a while until my hands didn't ache so much. And that was merely because I was holding them so tight and didn't use that muscle-action anywhere else in my life.

Likewise when I got my TT bike, new position and my shoulders and neck ached. They still do when I haven't been on it for a few weeks.

Just suss that out before you alter your bike too much.