Discolouration, sour taste, and inconsistent brew from one bottle to the next sounds like infection to me. I've had that happen before with a few brews, didn't let some bottles sanitize long enough. As far as bottling itself goes, even if you were storing the brew in green bottles out in the light, I really doubt it would have changed your brew as drastically as you've described it.
Hope the whole batch isn't ruined!
edit: oh, and how's Covington? I grew up in Slidell