mtparki said:...1 Would I be better off with a bike with 2 or 3 chain rings on the crankset?...
That depends on the terrain you'll ride in during training and racing. If you're living and will be racing somewhere flat then you won't get much use out of the granny gear on the triple. If you live in the mountains or somewhere with frequent steep climbs that take much over a minute to climb then a compact or triple makes sense, especially if your commute is hilly and you want the option of an easy cruise to work from time to time.
Quoted post said:...2 Should I get a bigger chainring (eg 52/39) or smaller (eg 50/34)?...
Again terrain is really important here, but the compact crank (50/34) paired up with a 11-25 rear cassette is basically best of both worlds in terms of a very high top gear for race speeds on steady descents or with big tailwinds and low gear for climbing and commuting. If you live and ride on flat terrain then the 52/39 or even something bigger like a 55/44 is nice for racing but a little steep for round the town commuting most places including flat places with frequent strong winds.
Quoted post said:...3 The bloke in the shop reckoned for a few hundred dollars more, the best thing I could do would be to get a better wheelset...
Cyclists love new wheelsets, but IMO it's not your best bang for the buck on your new bike. Moving to a road bike with a basic 700c wheelset and decent clinchers will be a huge improvement for training and racing on the road. Spending some money on a professional bike fit (more than the stand over the bike in the shop fit you get from some sales folks) is a better use of your funds. As are decent cycling clothes including shoes with a good clipless pedal system.
If you like the road bike and want to focus on improving your triathlon bike splits then a pair of clip on aero bars (and again a professional fit from a tri bike fitter) would be a better investment than a wheel upgrade.
Bottom line, you can get a very good raceworthy bike with your budget. Don't get caught up in the hype of needing to mortgage your house to buy the latest bling supermachine. Get something decent with a road race geometry (as opposed to a bike tailored for loaded touring or a cross bike, etc.) and spend the money you save on a professional bike fit and key accessories like good pedals, cleats and shoes as well as several pairs of cycling shorts and jerseys and essential items like a patch kit and pump/cartridge for the eventual flat tires.
Good luck,
-Dave