Nice commute! To get elevation gain, I ran your route through bikely.com. Bikely says about 800' one way and 1000' the other. Bikely exaggerates the climbing a bit, but that's still a lot in 8 or 9 miles. Even so, it's probably only an hour's ride. So take a 24 oz. bottle with plain water, and refill it at work. Lighter is better. When one is starting to do a hard commute, it's best IMO to use a recovery drink. Either take a bottle of Ensure and drink half of it as soon as you get to work and the other half when you get home, or use a powder like Recoverite or Endurox. Once you get stronger, this won't be so important because your body will become more efficient at using and storing water, electrolytes, and nutrients. See DJ's post.
If you commute 5 days/week, that adds up to about 9000' of climbing, nothing to sneeze at. In general, if your legs hurt while you are riding, you need to rest a day or so. If you find yourself using smaller gears than usual, the same. If you are using the same or larger gears, nothing to worry about. If your legs only hurt off the bike, nothing to worry about.
So what happened with the heart? HRM transmitter problem?