If she threw up at 4am, out of the blue, it could be bc she was a bit too hungry/tummy empty for too long. What time had she eaten dinner the night before? If she is vomiting early in the a.m., it may mean she needs a snack before bedtime.
When you say "homemade food" - are you supplementing and everything? If not, the upset could be bc of an unbalanced diet too. Which Natural Balance are you feeding? It's a fairly decent food - so I wouldn't think it would upset her unless there was an allergy or something. How long has the vomiting thing been going on?
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