Let's see, 3 to 4 day trip from Flathead and some neat scenic roads. My recommendations would be HWY 93 South to Hamilton MT which is about 120 miles (from Polson). Then take off east on HWY 38 (Skalkaho Highway) and stop off in Philipsburg for the candy shoppe (if it is still open, have not been that way in some time). HWY 38 has some nice driving with good scenery and sweeps. HWY 38 will turn into MT-1 / US 10-A and wind around Georgetown and Silver Lakes, ending up in Anaconda MT. If it is still open Haufbrau was a good German restaurant with some nice beer on tap.
From Anaconda it is a 30 mile drive to Butte on I-90 and from there you would take HWY 2, (Old US HWY 10), or Harding Way for those that live around them parts. That is a high mountain road with sharp twisties and not very busy. After you pass over the Continental Divide you will then go South on HWY 41 to Twin Bridges then take HWY 287 South to Sheridan, Alder, and then Virginia City where you can sample candy from the candy store there. (Note what drove most of my rides). Follow 287 to Ennis then continue south (I cannot remember the name of the HWY, I think it is still 287 S) following the Madison River. Then you can go East on Hebgon Lake Road and see the drowned trees at
Quake Lake. Once you reach the junction for HWY 191 go south and into West Yellowstone. Total distance is +/- 380 miles.
But that is just my suggestion