I'm surprised that the first guy didn't tell you that they could order the right size for you. It's a good thing you went back and got a competent person. I think you made a great decision, and will be very happy with your new bike.
For the numbness, chances are you're putting too much weight on your hands. As your core builds up for cycling, these are the muscles you want to use to hold you up. Get some good cycling gloves, and make sure your arms aren't locked but have a slight bend. Lighten up the weight on your hands by using your core muscles to support yourself. You should be able to get rid of the numbness in a very short time.
The bike itself doesn't need any upgrades unless you choose to. But the first thing you may want to change is the saddle, unless Cannondale made a significant improvement on the 2013 model. The older saddle wasn't bad, just pretty hard and had to be set just right for any kind of comfort. The stock grips are ergo and very comfortable. I'm able to use mine in a way that I can get various hand positions, which helps alleviate any numbness. A good wireless cyclocomputer can add a lot to your workouts or excursions.