Perhaps the bike doesn't fit you correctly and that is why you are hainv pain issues? That is a lot of flats in such a short period of time... but shifting and brake issues are to be expected when you first get a bike. You don't have hardly any miles on it. It takes time to get the cables stretched out. Surly your LBS explained this to you?

I have no experience with those particular tubes. I use Specialized road tubes and haven't had any issues. I have about 1200 miles on my Allez Elite with no flats yet... gf has a Dolce Elite with about 11 miles on it, no flats yet.