I did the Willamette Valley Scenic Bikeway last year as well. I took the short-cut that avoids Brownsville (just like Jeff suggested), but for the most part I kept pretty faithful to the most current route.
As for Willamette Mission, I heard a rumor that the park rangers will allow through cyclists to camp there. Don't know if its a fact, maybe next time I'll try. (and I hope they build a hiker/biker site soon!)
The biggest problem I had with the route (besides the lack of signage through Marion County, at least when I biked it in August of 2009) is there's NO LEGAL PLACE TO CAMP between Champoeg and Willamette Mission to Brownsville, which is a distance approaching 100 miles! I don't think most people want to push a century between campgrounds. I was fully prepared for the possibility of stealth camping, but I found a motel room in Albany for cheap (and it was starting to rain.) Hopefully they'll figure out something, ideally between Salem and Albany.