The reach of a 48 cm CAAD 8 should be fine, maybe even a little short with the stock stem, for a 5'4" woman with a long torso. But I can empathize with your consternation about the lack of straddle clearance. Also, I'm thinking you might have difficulty getting the handlebar low enough, especially if your arms are at all proportional to your torso. Unfortunately, riders with non-average proportions have to put up with all sorts of compromises when fitting themselves to stock road bikes.

I'd certainly talk with the shop owner about how you feel. Were I in his situation, I'd gladly set you up on the bike you bought and the smaller edition, as comfortably and properly as I could, and let you ride them both for a day. A 44 with a longer stem and a little persistence with the fit is not an outrageous request. The last thing I'd want is a customer who is not confident she made the right purchase.