I am not familiar with travel in WA or most of central/southern ID, but I have lots of familiarity with southwestern MT. I would individually view your origination/destination points as grand opportunities to see lots of southwestern MT and adjacent snippets of ID.
From Lookout Pass where I-90 enters MT from ID, you're just short runs from all grades of NF CGs and disbursed camping for most of the distance to Missoula.
From Missoula, US 93 south takes you through the rather heavily developed (by MT standards) Bitterroot Valley, but you pass by many highly glaciated canyons entering the Bitterroot Valley from the Bitteroot Mountains on the west.
At Lost Trail Pass go east on MT 43 and in a short distance enter the Big Hole, arguably the most spectacular alpine valley in the Lower 48. Bannack, MT is a well-preserved ghost town which was the original capital of Montana Territory in the 1860s. From Bannack you may connect with the Big Sheep Creek Backcountry Byway, a 55 mile gravel road excursion looping over to I-15 at Dell, MT. South on I-15 for 25-ish miles past Lima to Monida and hook east on MT 509/South Shore Rd all the way through the Centennial Valley for 60 miles to Red Rock Pass and return to ID there by Henry's Lake, just north of Island Park.
On this route you'd want to top off fuel in Hamilton or Wisdom MT and Lima MT, as I've recently read there is no longer fuel available in Jackson MT and it's been decades since fuel was available in Grant MT.
A very nice alternate would be continuing east on I-90 for 25 miles past Missoula, then south up Rock Creek via Rock Creek Rd. The first 10 miles of Rock Creek Rd are paved and somewhat developed, but that's followed by 30 miles of graded gravel FS road 102, steep and with tight switchbacks in a couple of places (but not so tight I couldn't get my longbed CC Superduty with 19' popup camper in tow through them), to MT 348 west of Philipsburg. MT 1 is a paved 2-lane highway from Philipsburg to Anaconda MT where you can pick up MT 569 over the Divide and back into the Big Hole at MT 43. Turning east for a few miles there gets you to Wise River and the northern end of the Pioneer Mountains Scenic Byway, a 40 mile paved, smooth parkway cutting through the middle of the Pioneer Mountains. Its southern end is at Polaris MT where it connects to MT 278 not far outside of Bannack. The "rub" about this alternate is you don't get to see the full majesty of the Big Hole between Wisdom and Jackson, so turning west/south towards Wisdom at the southern end of MT 569 out of Anaconda is a fine route, too. For either of these alternates you'll want to top off your fuel in Anaconda. I think fuel is available in Wise River but not positive. There is definitely no fuel along the Pioneer Byway nor beyond it, all the way to Lima, as described above. I think Wisdom always has fuel, albeit likely rather more expensive than in Hamilton, Anaconda, or Lima.
Oh, and going through the Big Hole between Wisdom and Jackson gets you reasonably close to Twin Lakes and Miner Lakes, two spectacular NF CGs on the west side of the Big Hole. Twin Lakes is about an hour's drive for the 20 miles to get there from MT 278, but it's SO worth the time/distance. On the other hand, the Pioneers Byway accesses 7 or 8 NF CGs along its length. But there, you may expect rather more larger campers and RVs given the high-quality paved access. Twin Lakes and Miner Lakes are 20 and 10 miles, respectively, up gravel roads and are each at the "end of the road" where there are no drivable through routes into ID from either access road off of MT 278.
Foy
