1. I second the recommendation of just going to a shop, talking with the staff, and looking at a bunch of bikes to determine what he wants/needs bike-wise.
Fenders, a horn and/or bell, and front and rear lights are the only things you'll really need to add on to the bike initially.
2. http://ridethecity.com/ is an excellent resource for route suggestions. Google maps is good too. Neither is perfect, and I often use a combination of the two plus my own knowledge of the streets.
3. I found I didn't need any special clothing - aside from my helmet and gloves - for my ~2 mile commute from Greenwood to Greenlake. I just rode in my regular clothes. If he's committed to riding rain or shine, he'll probably want some sort of rain gear, but he doesn't need to get all spandexed-up for such a short commute. Some padded shorts will make longer rides much more comfortable.
Sorry to be short on specifics. People are so individual in what they require comfort-wise and those needs will change as he rides more. There is such a huge array of products designed to facilitate riding that almost any issue can be addressed with a tweak of gear or components. Develop a relationship with a bike shop, maybe look online at forums devoted to bike commuting to see what lots of other folks are doing and just...ride like you belong on the road.