+1 on all of the above, epically the get the problem fixed and don't just assume you'll "get used" to it. Sounds like an injury waiting to happen if you continue... ibuprofen is your friend!! LOL. A little discomfort is one thing, but shooting pains mean something is wrong, you need to get it resolved.

First ride out on my new flat handlebar ride and a half mile in I was in a serious bother with bum and wrist pain. I stopped and moved the seat down (was too high and I was using my hands to support myself) and while it was better, the wrist was still very tender and painful. The LBS crew suggested to start with a slight tweak to the grips and rotated my Ergo grips back toward me about 10 degrees. I haven't done any long trips on this bike yet, but the wrist pain is gone, tho I am still working on the saddle angle as I feel sometimes I'm still slipping forward.

Good luck!!
Shannon