Several years ago I took a trip much like yours except I was lucky!  Rode from Portland Or. to Illinois on my 650 and the first rain I ran into was in Fort Dodge, Nebraska. Idaho was pretty and felt like you stepped back in time 50 years.  Wyoming was boring and you could ride for a long ways without seeing another vehicle on the roads. Only 500,000 people in the state. Horrible roads too but nothing like what Nebraska had to offer!  I agree the Methane smell gagged me and at the end of the day I smelled like poop. I had to shove a rag soaked in whiskey inside my full faced helmet to keep from throwing up. I met this guy who told me when he was in high school and the kids got bored they would have Huff parties where they would take a plastic one gallon milk jug and cut the bottom off. lay it over a fresh cow pie and take deep nose hits to get high!  The Sand Hills are windy and scary. Traveling 60 to 65 mph I would ride the center line and the gusts would blow me all the way over to the outside of the lane. Not much to see either except cow, and windmills which were everywhere. Spent about a week in Sioux Falls Iowa visiting a friend, and we rode on into Illinois where we set on the Mississppi on a warm afternoon and drank a beer and smoked a cigar and watched a couple of old paddle steam boats go by. My friend headed home and I was on my way to tour some Civil War battlefields on the East Coast but they were having record rains so I decided to go elsewhere. While sitting out a rain squall with another rider in this rest area we were robbed by a car load of punks. Knew we were in for some trouble when they got out of the car, pouring down rain with no shirts on and tattoo's everywhere. We were the only people other than them  in the rest area. They stole my helmet, jacket, camera, $350 in cash  and some other small stuff. I had my debit card stuffed in my sock.  I lost a tooth and had one chipped and ended up with a black eye that swelled shut. While sitting on the picnic bench being checked over by medical staff and the police, a darn bee stung me in the throat!  At that point I decided to head back home so I turned around and from that point on I had the best time of my life!  It was no longer about how many miles I tacked on but the people I met and the experiences along the way. It seems people like travelers, especially those traveling alone and I ran into many of them. The cops in Illinois gave me a beat up old helmet with a face shield duct taped on and a coat 2 times too large but served the purpose. When I made it back to ONeil Nebraska the rain and wind started so I decided to stay in a motel with a connected restaurant. The manager was a church member, which most are in the Midwest it seems because churches are almost on every block. I told him I wanted the cheapest room they had available and I told him my story. I guess he took pity on someone in a duct taped helmet and since I no longer had a rain coat, I was wearing a black plastic garbage bag duct taped over my coat and bread bags taped to my feet. He let me have the room for free and when I got up the next morning there was this cardboard box outside my door that some of his parishioners left for me. A better coat, some rain gear, a envelope with a $100 bill inside and another with $40 and a free breakfast voucher in the restaurant. I tried to give it all back because I did have my card with me but the people in the restaurant would not allow it. I was kinda embarrassed because they said a prayer for me and all they asked is for me on the way out of town to stop by this church and give thanks to this statue of Mary in front of this Catholic church. not being terribly religious, I did anyway and it must have worked because i was getting ready to ride back across the Sand hills and it was once again gusting really hard. i got about 10 miles out of town and decided to head north into South Dakota with the wind at my back. I rode across highway 44 so to avoid highway 90 which everyone was traveling 80 mph and spent the Memorial weekend in Rapid City and went and saw the National Monuments which tons of bikes were out from Sturgis and they took a liking to the little Savage and invited me back to Sturgis with them for a BBQ. Nice ride and rode with a bunch of maybe 50 bikes which was kinda scary since it was my first group ride but I made it and had a blast. Went to this cool Harley Davidson motorcycle museum while there. Rode into Deadwood, the home of Wild Bill Hitchcock and Annie Oakley, went and toured the wounded Knee massacre sight and rode thru the Badlands then on into  the Black Hills a day or so later and the weather was nice and the scenery surprised me. I always thought SD would be ugly but quite the opposite. Rode thru Montana which was kinda boring on the east side but the west side was some of the most beautiful country you will ever see anywhere. Spent a day at Custers battlefield and it looks pretty much like it did the day the 276 calvary soldiers were slaughtered. If you ever go to Montana there are two things you need to check out. Flathead lake which is one just north of Missoula. I did not even know it existed and out in the middle of nowhere is this lake that will make you swear your at the Ocean! Something like 50 miles long and 30 miles wide. Kept going and ran into the highlight of my trip, Glacier National Park almost on the Canadian border, You can not ride 50 ft without having to stop and take a picture. Check it out on the net sometime and you will see what I mean. From there I rode back across the pan handle of Idaho into Spokane Washington, dropped down into Oregon and followed the Columbia river back to Portland. I was pretty sad that my trip was ending and I knew it was a once in a lifetime experience that not many get the chance to do. I was going to share my riding experience  in here with everyone on my ride each day but like I said, my camera was stolen and I was not sure anyone would have wanted to read them anyway. But I still have my pics from my ride back and maybe someday I might even post them. In all, I put almost 7,000 miles on my Savage in just a little over a month and it ran like a clock and got me back home with not one problem at all except for my license plate falling off in Cody Wyoming which caused me to get pulled over quite a few times thru all of the states,  but never was cited for it because I had proper identification for myself and bike. best time of my life except for the birth of my son and I would do it again on my Savage except with 54,000 miles I do not think it would relish the journey as well as me.
Like I said, I had many great experiences but one even worse than being robbed in Illinois that caused me so much grief when I got home I plan on backtracking to a couple of places and make things right. I hope!  A story for another day!  Sorry for the long post!