Those are all good points. I biked most of the route while I was home (the hilly parts anyway.) The commute sort of breaks down like this:
7 Miles no traffic a few steep hills but nothing killer
3 Miles Moderately busy good sholder
5 miles no shoulder busy but good site lines and regular bike use. (this is HWY 99 from Creswell to Goshen if anyone lives around Eugene OR)
the rest is in Eugene; good shoulders, bike signage etc.

As to the work thing: I feel like if I am on time mostly then if I get a flat NBD; if I get a flat the first time I will never live it down. I need to build up some cred with my boss on that one. The bike came with commuter style tires and protectors, along with lights, tools and a spare tube (the guy was a boy scout I swear). So I think I am good to go. When traveling I assume an average speed of 10 MPH while my actual SOG is around 14 for long distances. That gives me enough time to not stress and enjoy the ride.