Not sure what you are saying about the lines - simply remove the strokes in teh appearance palette. In fact your sampling issue could relate to your awkward use of transparencies. Otehr than that I can't see anything that should prevent the sampler from working, but you never know...
I'm fairly new to illustrator, so I have no idea what I'm doing with transparencies that is awkward. Where am I making these mistakes, and how can I change it to be less awkward?
Also, what is 'removing the strokes in the appearance palette'?