The Indian Railways had 17 zones at last count. Life was simpler in the past. In 1963 there were only 8 zones as the SCR was yet to come.
The All-India timetables of those days used to carry a list of Inter-Railway junctions. It was quite a long list, but it was swollen by the 9 Non-Government light railways which had their space at the end of the timetable. In the timetable of October 1963 they were:
Dehri Rohtas Light Railway (DR)
Arrah Sasaram Light Railway (AS)
Futwah Islampur Light Railway (FI)
Howrah Amta Light Railway (HA)
Howrah Sheakhala Light Railway (HS)
Shahdara Saharanpur Light Railway (SS)
Ahmadpur Katwa Light Railway (AK)
Burdwan Katwa Light Railway (BK)
Bankura Damodar River Railway (BD)
For more about them you can see these earlier blogposts:
Here you can see the list of junctions given in the All-India Timetable
Note that the ones in bold type are the ones between regular zones. Some comments are given on the right.
Many changes occurred over the years, starting with the formation of the South Central Railway in 1966 with two divisions of CR and two of SR. A further adjustment was made between CR and SC in the 1970s. And the great reorganization of 2002-2003 brought the number of zones to 16 (though the Konkan Railway is not a zone) and then 17 when the Kolkata Metro became a zone.
And all the light railways were either closed or incorporated into the main zones.
Balharshah was not an inter-railway junction prior to 1966, but now it is.
Raichur had been an inter-railway junction right from the 1870s, but now it is not.
Waltair/VSKP remains an inter-railway junction since the east coast line was opened in the 1900s.
Kuchaman Road itself is closed when the route was re-aligned to be further away from the Sambhar Lake. Then the WR and NR joined at Phulera. And when the NWR was formed, there was no need for an inter-zone junction there.
One more point is that there were many junctions between the NR and NER in UP. At that time NER was almost entirely metre gauge. In most cases there were separate stations and station codes for the NR (BG) and NER (MG) stations. For example, Bareilly Jn was BE for NR and BRY for NER.