The Thun Trail crosses the Sch R. at the "Lionel" RR bridge by Rdg Area Community College. You then continue on the trail up along Front St (after going under the Penn St bridge) or whatever they call the newer blvd close to the river and then enter the wooded riparian area along the river again. This takes you under Buttonwood St bridge and eventually up to the Rt 183 bridge. Get on the 183 bridge and cross. Take the first possible left and go a block or so to pick up the trail entrance again. The trail then winds past "the point" at the Tully and continues up along the Tully through Stonecliff Park and beyond. I've never had any incidents, but I have a friend who had one on the "Lionel bridge." As I recall some guys wanted to rob him.
Ahh, now I found the articles. The incident that you mentioned was close to the very same "Lionel" RR bridge.