We haven't gone from Custer to East Glacier, but did drive there from Yellowstone a couple of years ago. Since there have been no other replies, I'll throw out a few suggestions for your consideration.
From Custer, I would head up to I90, with a stop at
Devil's Tower, assuming you haven't already been there. Right beside I90 in Crow Agency MT is the
Little Bighorn Battlefield. At Billings MT I would take routes 3, 12, 191 and 87 to Great Falls. Streets & Trips shows these roads to be between mountain areas.
Great Falls has the
Lewis & Clark Interpretive Center, which we found very interesting. Adjacent is
Giant Springs State Park, one of the largest springs in the world. We also drove to the base of
Ryan Dam at top of one of the original great falls of the Missouri. At the time we were there, it was spring runoff and the water was going over the top of the dam. There is a picnic area on an island below the dam. If you go take the toad due to steep grade to base of the dam.
When we drove from Yellowstone to east Glacier, we used route 89 to join route 87 to Great Falls. It was a nice scenic drive with one easy pass to go over. We camped at the
Great Falls KOA. They had a nice nature trail there. Another possibility is
Dick's RV Park. It is adjacent to a major highway and we were concerned about traffic noise, so chose the KOA.
After Great Falls, we took route 89 up to Browning. Lots of folks recommend route 464 north out of Browning to Babb, then south to St. Mary. This avoids some grades and curves on route 89. We went a little north of Browning and took Starr School Road to rejoin route 89 to St. Mary. This cut off some of the grades and curves. Nice scenic drive. We stayed at both the
St. Mary KOA and the NPS campground at Many Glacier.
BTW, we lived in Alamo MI for 4 years back in the mid 70's. We loved it there. I worked at American Cyanamid (now Cytec Industries) on Miller road. Not far from Portage. Small world.