I think you are on the right track with linking the changes to her poop and the milk. I would definantly be questioning the cows milk. For those with sensitive little guts, cows mik is extremely hard to digest. Usually its the proteins in the milk that cause problems, and usually the LO's will have an intolerance to the proteins. Most will outgrow this as their gut matures.
Check out the stickies on the food allergies board:
http://babywhispererforums.com/index.php?topic=185707.0You can try some more digestible milks:
A2 cows milk
goat milk
raw goat milk (unpasteurised) very easy to digest as it contains all the enzymes and beneficial bactoeria, but you need to trust the source dairy farm and buy organic if you can. I mention this because my son is near allergic to milk and had a severe intolerance to dairy but he tolerates the raw goat milk.
Non- dairy:
oat milk
soy milk
almond milk
As for yoghurts, buffalo yoghurt, goats yoghurt and sheep yoghurt are all the A2 protein so much easier to digest. The buffalo yoghurt has to most benefical fat and most calcium of the lot.