Whoever said commuting requires more sleep is.. very correct. I can see direct correlations with my rides and my sleep schedule. The past two days have been very long work days for me, and while the riding has been pleasant, my legs have been light lead. Not full-on lead, just the lighter stuff
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Good luck on the knee, one of mine was bothering me, but I suspect it was mainly due to my new commute route - which is quite hilly. Two weeks after starting the new route, the knee no longer seems to be bothering me, here's hoping you have the same luck.
Also regarding tiredness, I know that I am slower commuting - even if I'm on the "fast" ride home - as I have a backpack on me. I'd suspect loaded panniers would be the culprit in your case, but same difference, extra weight definitely is noticeable. I am always surprised how a 10 pound pack can alter my speed. In fact, I've stopped carrying my laptop (with the carrier and accessories it probably weighs in around 10 pounds) with me, as I will literally drop 1mph average over my "long" commute, and arrive noticeably tired. I learned this same thing hiking, as it's amazing how much difference even 5 pounds will make.
Finally, good luck and enjoy it. I love bicycle commuting, there are days where I make excuses not to like yesterday (which was a good one, I was at work until 1:30am and was headed back at 8:30am), but for the most part I love it. A great way to start the morning, in my case.