I think that before Spa Road we would have passed the station of Blackfriars Road. The stairway entrance is still visible under the bridge, labelled "Charing Cross Railway - Blackfriars Station"
Commercial Dock
I admit to being slightly dubious about this one because it was almost on top of the junction between the London & Greenwich and London & Croydon/London & Brighton Railway. I will do an OS map check.
Update - unfortunately I can't find a map of the right date. By the time of the construction of the later station of Southwark Park on more or less the same site in 1902, the Greenwich line had separate tracks but I don't know whether this was the case in 1856 when Commercial Dock station was built.