Kelly,
You quote the current FRA web site but it is a 1977 rule that is quoted. I think the key wording is, and "When a train stops on main track, flag protection against following trains on the same track must be provided as ..."
Since the C&TS has no following trains, is flagging required? Also, CSX has outlawed the use of track torpedos, so I assume that the FRA reg. cited above cannot be current, or else the wording "each railroad must have in effect an operating rule:" may allow the railroad to use their own rule as a replacement.
Anyone in the know here who would care to comment?
Regardless, it sounds like common sense should dictate that the conductor or flagman should be equipped with red flags, fusees and a lantern, as well as a radio.