Have you taken a peek at the website RefluxRebels.com? it is really helpful to get an idea on if it could be reflux, or mspi, or both. My DS was recently diagnosed with MSPI, and has had reflux since birth. Now on Prevacid and a new formula, he is doing MUCH better!
Until he went on a hydrolysed formula, nutramigen, he was projectile vomiting (way more than the normal reflux spit up) and his diapers sound exactly like your daughters - dark dark green and extreeeeeemly stinky! I found out later, that these are both MSPI related. Have you noticed any mucous in them? or blood spots? I know its hard to see in such a dark color, but once I knew what to look for, It was easy to spot. they even have pictures (I know thats weird and gross, but actually helpful,lol) on that website. But that is a huge indication of food allergy. After being on the new formula for about 3 days, he had his first non stinky diaper ever! Good luck, and good job looking out for your daughter!
B