It should be fine for racing as is. You don't need to upgrade the Ultegra unless you have cash burning a hole in your pocket and you want to shave every gram you can. You MAY want to consider asking the shop if they would swap out the crankset for a standard double (usually they will give you a substantial credit for this, so you are basically just paying the difference, but shops vary), since you may want higher gearing for racing, but then again you may not. In any case you'd probably be better with the compact than with the triple.
Switching the wheels for a lighter set would probably be the biggest payoff for the money, but you can do that any time and don't need to be in a hurry, you could definitely race on the heavier wheels until you feel like you can justify buying lighter ones.
My bf has a 2007 Madone 5.2 and did not have a good experience with the stock Bontrager tires... and you will probably have to replace the seat... but depending on the deal you are getting, I would say it looks like a good bike. I don't think you'd have to do a lot of upgrading. Of course everything could always be lighter, and eventually you might be making some non-necessary upgrades like carbon bars, lighter stem, lighter seatpost (though I'm not sure how many options you have for the seatpost on the new Madone, come to think about it), etc, but that's another story...