If all the blood work looked good it means that the liver and kidney functions should be normal since the liver and kidney functions are usually checked when routine blood work is performed.
Have X-Rays been performed? These are usually done prior to having an ultrasound done. An ultrasound is not invasive and could give you some good information, however, it can be costly.
Have you tried giving her pepcid or zantac when she first gets up? Some dogs just have acid reflux as some people do, so pepcid or zantac would lower the acid and stop the relfux. If she has inflammatory bowel disease a low residue diet would be a good choice. This is a prescription food, that your veterinarian should have.
Thank You for your response. It was most helpful.