A couple of thoughts....try to park the bike in your office just for piece of mind during the work day. If you can't, consider something like PitLocks (
http://www.peterwhitecycles.com/pitlock.asp ) for the wheels, seat and stem (keeps the front wheel from being removed). Then a mini u-lock from the frame to the rack is probably all you need. The mini locks are harder to pry open, although they can still be cut.

Note: I have a custom Waterford commuter (my commute is about 25-30 miles round trip and I am a year-round commuter). I have the luxury of secure bicycle parking, but I run with the pitlocks and use a mini-u when I stop for groceries.

I don't carry any more than you, but I do carry 2 tubes plus a patch kit. While my RiBiMo tires have been solid, I believe some of the cities I traverse through believe that crushed glass is an appropriate paving material. With 2 tubes I feel more secure.

Good luck on the commute. May you reach the point where driving a car to work just "feels wrong".