D.W.
Howdy!
I am a Pedi RN and we get calls about this ALL of the time! I very seriously doubt that a minor (speaking as a nurse not as a mom!) head injury from 2 years ago would be causing problems now. Your Pedi would be watching for things like loss of developmental milestones, stomach aches that lead to vomiting, etc... . SInce you have already spoken to your Pedi you should relax! If you really want to you can always ask the DOc to order a CT scan and offer to pay cash for the proceedure.
I would suggest keeping a log of when she has the Headaches and stomache aches- see if after a week you can determine a pattern- is it right before she eats? Is it ALWAYS around the time she is suppossed to do something she doesn't want to do? Is it within an hour of drinking milk or eating dairy (might be related to a lactose intolerance).
My standard line for my daughter (who is 5 1/2) is to tell her that I am sure laying in bed for awhile will make her feel better. After being sent to bed a few times she has become much healthier!
Feel free to e-mail me w/ any other questions!
D.