Couple of quick thoughts. As far as rust prevention goes, invest in a can of "Frame Saver", should be around $10 or less. It is something you stray on the inside of steel frames which coats and protects the frame from rusting. It is a little work to do initially, but will be worth it in the long run. You might ask the shop to do it for you, they'll probably charge you, but you might be able to negotiate that labor if they don't budge on price.

As far as the clipless pedals, most bikes(exceptlow end bikes) don't come with any pedals because they are a personal preference item. So, if they don't offer the pedals, give a "gee, I thought the pedals came with the bike" and maybe they will throw them in.

As far as haggling, just ask in a respectful and sincere way. Bike shops are used to people always trying to haggle. Money always talks, so if you can pay cash for the bike and have a wad in your pocket, it always helps in the negotiations. Also, I would check around for a comprable close-out bike (or this year's model) at another shop and tell them you are wavering between the two of them and ask what their best deal is because that will be the deciding factor. It always helps to be able to walk out if they don't want to budge (even if you know you'll be back) - tell them you are going to go look at the other bike again.

Well, not sure if that qualified as a couple of quick thoughts, but good luck!