Looks like some great preparation. I didn't read all the details and maybe you've covered this, but here are a few important things I have found on trips like this.
For the GPS convert your routes to tracks and plan to navigate by following the tracks.
If you haven't done a lot of this type riding, I would recommend practicing navigation. I have always found it a lot harder than I would ever have believed. Things just don't work the way you think they will. Using tracks solves a lot of the problems.
There were lots of major-looking dirt roads in Oregon that did not show up my GPS at the time.
Instead of the thumb drive, you might just buy another microSD card and just swap it out if you have a problem.
Plan on having to do maintenance to your air filter. I carry two preoiled spares for my KLR.
Bring a small voltmeter. You can get one for less than $5 at Harbor Freight. I have found I use this about more than any other tool on trips anymore.