In some small defense of Petco, I got my current guinea pig from my local Petco branch because the piggies at the other two pet stores in town looked really awful. The Petco ones looked happy and healthy and their cages were clean, which is more than I can say for the other pet stores. There aren't any breeders that I am aware of in my area, and I honestly don't know much about aquiring from a breeder, but I've had pet store piggies all my life and never had problems with them that were related to the place I got them from. Not that I support Petco's chain-store profit-driven approach to selling animals, but in some cases it may be the best option. For me, I always buy from stores that consistently provide clean living quarters with plenty of food and water, and whom I never see selling animals that look sick. I am also sure to give them a thorough inspection for signs of illness before buying. It is true that pet stores typically have their pigs in cramped quarters with no hay or fresh things for them to eat, but then most piggies are only at the store a few weeks at most. All that is just a long way of saying, Magic8Ball, don't feel bad for getting a piggie from Petco.
For the record, all the piggies I've gotten from pet stores took awhile to warm up to fresh veggies, and with each pig of course there were some things that became favorites and some things they would never touch. And some things that they woudn't eat at first, but that I wouldn't give them for awhile then try them again some time later and then they'd love it. Just like people piggies have individual taste preferences that change over time. So just be patient and persistent (but not pushy) and eventually you and Cornflake will both figure out what she likes to eat. With the water bottle, too, if it's different than what she's used to it may take a little time for her to figure out exactly how to use it. Also with just one piggy, especially if she's very young and the bottle very large, she may just not seem to drink much. As long as you see her drinking sometimes, she should be okay. Just keep an eye on her and figure out what "normal" is for her so you will notice if there are changes in her drinking patterns.
One final note on hay: "timothy" refers to the type of hay, not the brand. I had always used the Walmart and petstore brand hays (Kaycee or something like that), but after doing some reading today, I think I will be looking into finding a local feed store or ordering online for a fresher, better quality hay.
Glad to hear the vet caught the eye infection! What a bummer; I hope Cornflake feels better quickly! That's so funny she bit the storeperson; those minimum wage lackeys they hire in off the streets (actually I have no idea what the real job requirements are) in my experience are never very skilled or sympathetic at handling piggies. (Although I'd keep an eye out for the biting - in my experience I've never ever had a problem with piggies biting people except in cases where they were consistently mishandled or treated badly).
Anywho, I am by no means an expert, that's just what I've learned from my experience with piggies. Hope it helps!