The Thompson is one of my favorite smaller rivers. I haven't been up there in the fall, so I can't tell you what to expect. And it is a bit of a drive from Missoula, but a pretty drive at that.

Another option for smaller tribs to the Clark Fork is the St. Regis. I've only fished that once, from a raft with a local guide who gave me a free ride one day. What I remember most is how beautiful the streambed was - a tremendous variety of quite colorful rocks. Stunning, and I did catch a few pretty nice fish along the way.

Fish Creek is another Clark Fork trib, and much closer to Missoula. But I haven't done much there and haven't done well the few times I've fished it.

It does occur to me that all three of these tribs might host brown trout spawning runs, but mid-September might be a bit early for that.

You might PM Sagefisher, who has spent quite a bit of time on the lower Clark Fork on guided trips and probably has some good ideas.