My daughter woke up at 1am bad stomach ache. She was crying and she handles pain very well. She has been vomiting and now she feels ache and head ach?

Could be serious. Severe pain in the abdomen, with vomiting could be serious. Take her to see a doc soon, urgent care or er. This could be appendicitis, hernia, colitis, or a virus with dehydration. Good luck.
Seek medical attn. Waking from sleep with pain should be assessed by a doctor. She might just have a virus but she could have urinary/kidney infection, appendicitis, or other more serious infection.