The Bartram Trail ends short of an old iron railroad bridge before the trail would reach the village of Auburn. When the trail was built they were to re-deck the bridge. But the guy who owns the land on the other side of the bridge would not allow the trail over his land. Look at GOOGLE maps. Before you reach the blocked off bridge there is an access area on Pine Lane. You can take that Pine Lane to Bear Creek Road. Bear Creek Road goes into the village of Auburn. Puts you on Route 895 at Auburn.
Check a map for small roads up along the river out of Auburn. There is a very short section of trail near Landingville but not connected to anything. You should find a back road that goes up into Schuylkill Haven. Schuylkill Haven to Pottsville has no close to the river road or trail that I am aware of.
Between Hamburg, PA and Schuylkill Haven there is extensive work being done on Route 61.
If you are using the Thun Trail through Berks County the section above Reading is a lot of little used roads. One section that crests a hill was gravel the last time we were on it.