Hey man that's great that you are commuting!

If you are sore all the time it's your body asking for a day off. You'd be surprised how much more energetic you will feel if you give yourself a day, or two days, or three days off after every riding day. As you find that the muscle soreness improves you can then add another riding day. Think about measuring your fitness in terms of recovery time rather than excersize time. In the beginning, just don't ride if you are sore, that will control your ramp up quite nicely. Also with a few days off each week you will find yourself sailing through your commute and really looking forward to it.

To help scale your expectations, I took off 25 lbs over the course of a year by cycle commuting alone. That is 1/2 pound per week and I didn't make any radical (by that I mean unsustainable) changes to my diet. I didn't suffer and I still look forward to my ride.

Later,
HB