Bike Fit

So, I had a bike fit on Tuesday after work. It was a lengthy process but I could have stayed in the bike shop all afternoon. Oh wait... I did. The gal who did the fit for me was super great. She has all sorts of fit school certifications and is a triathlete herself. Sparing you all the numerous details, the trouble I ran into was that I am short (5'3"ish) and have disproportionally long arm and legs and a short torso. Now, you may think that this would correspond into increased power and therefore speed on the bike with decreased wind resistance, however, all it proved to be was a nuisance. To get into a moderately aggressive aero position with my shoulders at 90º where they are comfortable meant I was cracking my elbows with my knees. I will have to sacrifice some of knee over pedal spindle in order for the aero position to be alright. I am currently riding on a 54 cm Specialized road bike and was fit for a 47 cm tri bike. There were several bikes I can choose from but only the Trek Equinox 7 WSD has 700cc wheels in that size. All other bikes with that small of a frame ride a 650cc. I am also trying to make decisions on the aerobars (s bends or not) and the shifters (upgrade to Dura Ace). The last thing is do I want to buy new shoes, pedals, and cleats or switch out for awhile? Pretty sweet though, deciding on such a cool new piece of equipment.
P.S. I like powder blue but not necessarily on a bike. This may prove to be an advantage in transition as my bike will stand out like a Care Bear in the crowd!