Sounds like you had a thorough fit! There are still adjustments they can make. My hoods got fiddled with a lot, both rotating them in some and rotating them up some - it was huge.
Now, I'm not as small as you, but you may not be able to put a foot down easily and you'll just have to get used to it.
Before the trek haters come on board... I LOVE my madone. One of my buddies is very small and riders the 47 and is very happy.
2015 Liv Intrigue 2
Pro Mongoose Titanium Singlespeed
2012 Trek Madone 4.6 Compact SRAM