Congratulations on the new job - and the excellent opportunity you have for a great commute! Welcome to the club!
For breakfast I'll echo those who suggest oatmeal, fruit, toast/peanut butter, etc. Foods like that will give you energy without spiking your blood sugar - and help you arrive at work not feeling "depleted." Skip the 'replacements' if possible.
Your tire choice should be dependent on the conditions (road/weather/debris) you ride in. As Exile said, experience will be your teacher. There are lots of choices. Come back and ask us when you know more...
Backpacks and messenger bags usually lose their appeal after the 10th mile or so for me. I think you'll find a light-duty rack, a trunk bag and/or panniers will be more comfortable and pretty unnoticeable if you are carrying just a few pounds.
Good luck - and let us know how things go.