Glad she is running better. If you still have the oem plug caps, swap for some NGK replacement caps. As often as your bike has been worked on I am betting the oem bits insulation is failing and they are now arcing and the rain is adding to the problem resulting in the rough running.
Some beautiful places to camp all over that area and check out KOA Kabins if you find the need for more protection now and again, some areas are pricier than others, but they usually are much cheaper than hotels and do a good job.
Your bike troubles have caused you to miss some fantastic riding areas, I hope the rest of the journey allows for maximum exploration.