First, I'm bummed that we missed meeting in the office while you were in Missoula!
Second, I think you must have an older TransAm #4 map. Once the bike path was completed, we changed the route to do just as you suggest below:
The official AC route gets off the trail and crosses the river onto East Side Highway at Stevensville. No need for that. The East Side Highway is busy and has no real shoulder to speak of. Stay on the trail towards Hamilton.