Mark,
There are several places to stay in the Flint area. The Holiday Inn Express is good but you can't wander much on foot, the City has been pretty rough this year.
There are several options off of US 23 on Hill road around the Gateway Center. To the north there are several motels around the Outlet mall in Birch Run and in Frankenmuth itself. Frankenmuth is a tourist town and is priced as such but it does have a lot of family type attractions and it is close to Junction Valley.
464 will be running the whole summer except for the the end of June for a boiler wash (6/30-7/3) and the third and forth weeks of August for a boiler wash and our Thomas event.
Gook luck with your plans
Paul