I recommend you go on a bike tour!
Hope I'm not stating the obvious here, but you should probably do some guesstimating about when you will be where, and make sure you aren't in the mountains too early (snow) or in the desert too late (heat). Probably don't want to be in the rockies in May, and you should have enough time flexibility so that you can wait out a storm. Things are going to be colder up north.
weather.com has some seasonal averages pages that are very useful. Also do some searching on seasonal wind direction.
My gut reaction is that it could make sense with the climate & terrain to fly to SF and ride the Western Express eastbound. You'll have a couple of days in the Sierra that you will need to have good weather for, but it won't be as insanely hot in Nevada, and by the time you get to the Rockies things will have warmed up. Obviously there are other things to consider, though, so you're going to have to balance all the options.
And, if you run out of time, you'll be skipping the plains, which I personally don't enjoy much, as opposed to the mountains or coastal areas.
90-100 m/d is a very aggressive schedule, most folks average in the 60-70 range, if carrying camping gear. Don't forget to build some room into your schedule for bad weather, mechanical problems, illness, or just encountering something so darn cool that you need to hang around and experience it for a while. I usually build in one day a week of not riding.
Have a great time, whatever you decide!
and please, if anyone thinks i'm not analyzing this right, chime in, i'm not certain about the weather issues, just saying my guesses about it.