I think if you start out on an Adventure Cycling Route, that takes care of most of the planning for you. All you have to do is pay attention to how much food & water you need to get you to your next services, stock up, and ride.
Take it very very easy the first few days. The very first day, you may be a total spaz, you'll have a bunch of logistics to deal with - putting the bike together, fixing anything that is tweaked, etc., likely on little sleep (if you're anything like me) - so don't even plan a real ride that day. Fly in, get a hotel or campground in advance for that day, and get yourself sorted. The next couple day should be low miles as well, so you can get your packing system dialed in - you'll pack and repack a dozen times the first few days, then you can just keep doing what you figured out works from then on. Take a rest day before you are desperate for one, and try to pick a town that has at least a little of interest to you.
I can't tell you much about the hotel density (I've been on all those routes-ish except Seattle), but I have never not been able to find indoor lodging when I wanted it - which is usually less than once a week. BUt since it's win-win-win, and all those roads will be there next time you get a chance to tour as well, anything that helps you pick is fine. If you fell like the Portland start is the best one - do it!
I did Lewis and Clark starting in Astoria on 8/1, had a 30 mile-an-hour TAIL wind for the first 4 days, a few hot days getting to the Lewiston/Clarkston area, then perfect sunny weather all the way to Bozeman (where I continued east, you'll be trending south). I thought it was a lovely route.
