It sounds like what Gwen did, she was really wary of the breast for a couple weeks, sometimes I would have to put a little milk on my pinky to get her to latch. But pumping a little past letdown when I knew I was full and taking her off till the letdown past otherwise helped her a lot. After her 3 month growth spurt she was able to handle whatever milk came at her! I don't know about the milk stain, mine never had that, but if you aren't in any pain you probably don't need to worry. Thrush is VERY painful, just pay attention if it feels like all of a sudden she isn't latching right or your nipple feels itchy, those are the first signs.