Having a severe refluxer myself with FA's to everything under the sun, I don't think that's what it is. Yes, the night waking could attribute to some of that (in which case I'd give her some Mylanta Cherry Supreme to see if that would help calm her down- the juice will only add fuel to the fire since it's so acidic).
I'd do an elimination diet and keep her foods pretty bland and boring for the next few days to see if that improves things any. Then add your suspect foods back in one at a time and watch for her reactions.
Ellie just went through a milk trial a week and a half ago (can you spell "disaster"?!) so I feel your pain. We are avoiding: milk, soy, corn, rice, wheat, oats, pitted fruits, and meat. I more than feel your pain, sister!
As far as the Upper GI goes, it's the least invasive test there is. All they do it have them drink barium and then x-ray it going down and see if it's refluxed at all (a total of 5 minutes MAYBE). It's not bad at all. :) Ellie has had the UGI, Upper Endoscopy, Flex sigmoidoscopy, Rectal suction biopsy, multiple stomach x-rays, etc. etc. So really! Don't worry about the UGI if that's what they want to do!
Keep your head up!