6 one way, 1/2 dozen the other.
There have been a lot of guys that have taken the LC8 engine all over creation (Jean-Luc, Crashmaster, Misery Goat, Aurel) and never really had a problem. If a town doesn't have parts then UPS to the rescue. Obviously carry stuff you know you'll need like the water pump kit, maybe a sprocket set. Plus there are so many guys in OC that have done so much stuff to those bikes that if the Great Pumpkin goes down we'll likely be able to help you fix it.
The WR will be a lot nicer when the road turns to shit, you can kick it off of you if you crash solo, and from what I've seen those little bikes are bullet proof. A lot of Jap bike brands use the same parts so thats a plus.
Me, personally, I'd take the 990 because I know I can stand to ride it for days on end. Compared to my 250 XC-F which I think I would be sick of after a few days, and also to my 525 EXC that I made into a motard that after 8,000 miles I realized the seat sucked (better than the old KTM seats though).
It all comes down to you. What do you think you could stand to ride after camping in the rain, waking up wet and cold, and realizing you have to ride a bike for the next 6 hours?