If your knees are hurting that suggest that there's something wrong with the size/setup of your bike. Options include:
1. Seat is to low
2. Seat is to far back and you're sitting to far back (this happened to me recently as I played around with my fit)
3. You have bike shoes/cleats and the cleat isn't adjust right (it's probably to far forward on the shoe).


On the other subject, if you're looking for a road bike that's going to be comfortable, one bike I'd suggest looking at is a Specialized Sequoia:
http://www.specialized.com/us/en/bc/...=39270&eid=117

Skinny road tires and drop bars, but designed to be more upright (for a road bike) and be vibration absorbing. $880 retail price for the base model, which would be ok for what you're trying to do.