Nobody mentioned LEDs. Going full LED has really helped my battery out. I found it would loose charge pretty quickly (within a month or two) before I switched to all LEDs (including a Trucklite 27270C headlight, which is low power and bright, but has a crumby beam pattern). I was also running on an old battery, but bought a new one at the same time as the LED swap. Haven't had any problems since. Oh, I've also got a Dyna-S ignition with 5ohm coils, which draws quite a bit more power than the stock!
I have a similarly short commute as well (3.3mi or 5.3km), but I let it warm up for 1-2 minutes before I take off (start it up, put on jacket, gloves, helmet, 3-point turn in my driveway). I do a 60-count in my head to make sure I give myself plenty of time to get oil in the valve train. Another 2-3 minutes of 3-4k rpm through the neighbor hood before I get to a big street, then I keep it between 3 and 6 (I don't typically have many stops from home to work). By the end of the commute, I'll usually rev it up to 7k on the last stretch to keep those spark plugs happy.
On a side note: my bike doesn't like to hang out at 4000 all that much, so I'm usually between 3-3.5k or 4.5-6k. I'm still working that out. Additionally, I kick start it with full choke (parallel to the ground), kick the lever and immediately after give it some throttle. Springs to life, but often times dies after about 5 seconds if I don't hold the throttle to keep it idling. I also live in sunny Southern California, where its almost always warm.