(Added a few more based on inputs by Mr Ganesh Iyer and others).
Now we look at goods-only lines which connect ports.
The line from Obulavaripalli to Krishnapatnam port has been covered here: https://abn397.wordpress.com/2020/01/09/the-new-line-to-krishnapatnam-port/
There must be some crossing stations, but they are not listed.
Ennore -Ennore port:
Chennai Harbour (HOM) does not seem to have a connection to other stations in the area.
Note that this station is not the same as Karaikal (KIK).
Older timetables show local trains running from Waltair (present VSKP) to Vizagapatnam Town and then Vizagapatnam Port.
This had limited passenger services in the past when MG lines were still there. And even when NG lines of the Cutch State Railway served this area.
Next door, we have the ultramodern port at Mundra:
Even a separate station for the airport.
This had passenger services in the past. Long ago there were ferries between Navlakhi and Kandla.
Other port lines such as Hadmatiya-Jodiya, Jamnagar-Bedi and Khambaliya-Salaiya have been closed for a long time when they were still MG. Presumably they were not felt to be worth coverting to BG in the 1970s.
A BG line still exists from Jamnagar to Windmill which may be extended to Bedi port.
Kochi Harbour Terminus:
This was a busy passenger section in the past, but the conversion of the Ernakulam-TVC line in 1975 spelt the start of this station’s decline as a passenger station. Perhaps the last important express to go there was the 41/42 Cochin Express which continued till the late 80s (and was then extended to Alleppey).
Problems connected with electrification of the bridge after ERS played a part. A recent attempt to run a DMU between ERS and CHTS in late 2018 was deemed a failure-partly because of the long closures of LC gates. Goods services continued with diesel traction, but the original port lost much of its importance with the commissioning of the container terminal at Vallarpadam.
This is a new line built which branches off from Idapalli, before ERN.
Panamburu (New Mangalore port):
This line was built around 1970 and could be said to be the first step of the Konkan Railway from the southern end. The proper KR started from Thokur.
MRH had passenger trains in timetables of the mid-60s, though the important trains terminated at VSG.
Finally to Gujarat again:
This branch had passenger trains until the 80s.
Passenger trains still run up to Rajula City.
JNPT (near Mumbai):
There is no station named Nhava Sheva in RBS.
No station named Hazira either. There is a line accessible from Gothangam which reaches the Kribhco factory near Hazira. Presumably the line to the port is not complete.
We should remember that Mumbai, Kolkata and Chennai ports have their own railway systems which are not part of any zonal railway. Details do not seem to be given in RBS. Part of the KPT’s lines became part of the Kolkata Circular Railway.
However the lines to Mundra and Pipavav are part of WR.