I'm hoping that some Portland people, like dtrain, will step up with the best route from downtown to Champoeg for you. The times I've done it I've come from Beaverton over 219 to Newberg, then over the river to the park.
Here is an alternative route from Salem to Eugene that I really like. It takes you to Corvallis, which is a university town with a nice downtown with cafes and lots of people on the streets. From there I ride the foot hills to Bellfountain, then through the farms to Eugene. See what you think as an alternative to Albany and Brownsville.
http://www.gmap-pedometer.com/?r=5062250