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I just read your post and did not go down the list because I am in a hurry. The yellow is bile and comes up instead of going to the stomach just like when we puke.
It sounds like she had a stressful day with the microchipping and all. If not better in morning you should return to vet for a parvo test-diarhea and vomiting together scare me--dehydration is the real killer in many of the puppy illnesses. If she jumps around, eats and drinks, then all is fine and sounds like a temporary stomach and bowel upset, but if it persists longer than a few hours you must go to the vet ASAP.
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