These tips are really helpful. So much good information from folks that have done this before. I'll start out in Anacortes in late May. I'll follow the NT route until I get to Glacier. I plan on spending some time in MT and WY. First in Glacier, then head down to Missoula via the Great Parks North route, then down to Yellowstone/Teton via the TA route, back up to catch the Northern tier in Dickinson, ND via Great Falls along the the Lewis & Clark. Weather, time, or other route interests may change this plan. I've never done a tour where I didn't change the route a least a little bit for all three reasons.
Late May is when I started from Seattle both times. Three days up to the NT at Bay View, WA, a bit east of Anacortes. Don't know what the winter was like this year, but the winter of '98-'99 was really snowy. We got rained on then snowed on crossing Rainy and Washington Passes. Winthrop to Tonakset was quite warm. Then we woke to flurries in Republic and had more on the descent from Sherman Pass.
Howard Miller Steelhead Park in Rockport, WA has Adirondack shelters. Nice amenity if it's cold and wet like it was when we were there. This spring, construction will start on biker sites at Whitefish Lake State Park. Don't know when they will be ready, and it's my understanding from people that the train noise at the park can be disturbing.
In '00 I went to Glacier, rode up the west slope of Going to the Sun then back down, then backtracked to Columbia Falls/Whitefish and took the Great Parks North to Missoula. I then continued on the TransAm to Yellowstone and eventually ended up on Cortez, CO via the Great Parks South. I prefer Sprague Creek Campground in Glacier. It's within walking distance of the Lake McDonald lodge. If you don't mind being dependent upon the shuttle, Avalanche Campground might make more sense. Shop for groceries in W. Glacier, before you enter the park. The selection at the store at the lodge is more along the lines of "junk food."
In '11 and '14 I did two loops out of Missoula on the TA as far east as Twin Bridges. I will actually be back in MSO on June 14th for another loop that will take me as far east as Ennis before I head north and then west back to MSO. If you don't mind some (about 6.5 miles) of pretty easy gravel, don't pass up the Old Darby Rd. Alternative between Hamilton and Darby, MT. Great views and quitter than U.S. 93. Shop in Darby as the grocery selection at the Sula Country Store & Campground is very limited (the breakfast is good), and the store portion closes at 5 p.m. When I got there in '14 at about 5:02 the store was dark and locked up tight. This year I plan to stay at Spring Gulch Campground (U.S.F.S.), which is a few miles west of there, just for something different. There is a cyclist-only site there.
If you want a real dirt challenge, take Gibbons Pass east of Sula if it's open. I did it in '11. The west slope is narrow and rough in places, but doable with sturdy, wide tires. (I ride 35c.) But it really is like being in the backcountry, and it's shorter that Lost Trail/Chief Jospeh Passes. While climbing the west slope I encountered one vehicle. The east side is a totally different experience. Wide, mostly gentle grade with a good dirt surface.
The mosquitoes in Wisdom will eat you alive. In fact, there is a little climb about 8 miles before town, as you pass a ranch, where they are really bad. Groceries are relatively limited, but The Crossings at Fetty's serves up great grub. Didn't check on the condition of the screened shelter in the American Legion park. I pitched my tent in there back in '00. In '11 we got a motel room in town. (The GF wanted no part of the bugs.) In '14 I pushed on to Jackson and camped at the hot springs resort. Pricey (close to $30, IIRC), but that comes with use of the hot springs pool and a large towel, which is a nice treat. The food there is good, and there is another place in town, but no grocery store.
I know people often like to stay in Dillon, MT because of the size and availability of services, but I highly recommend the Bike Camp in Twin Bridges. First class facility in a nice setting along the Beaverhead river, and it's free (donations strongly recommended). The town also has a very good grocery/liquor store, library with Internet access and a couple of restaurants. The fishing access campground just outside of the center of Ennis was tranquil when I was there in '00. Plan to stay there this year.
Send me a PM if you can handle dirt (some of it rough in places) and want a really sweet detour off the TransAm after Big Hole Pass east of Jackson that ultimately takes you to Twin Bridges. There is a way you can do it without the dirt, but that way passes through Dillon on the way to Twin Bridges and adds even more miles.