The only books I have seen referenced are very old and hence mainly relate to the period before partition.
Hundred Years of Pakistan Railways: Pakistan Western Railway 1861-1961, Pakistan Eastern Railway, 1862-1962
Malik, M. B. K. Published by Ministry of Railways and Communications, Karachi, 1962
Couplings to the Khyber : The story of the North Western Railway
Berridge P S A Published by David & Charles (1969), Newton Abbot, UK, 1969
More recent is
My Years with Pakistan Railways: What Went Wrong with Railways in Pakistan ...
Mian Ghias-ud-Din Ibrahim Publishers, 2007
and
The Railways in Colonial South Asia, 2021 also has a couple of chapters on Pakistan post independence.
Not read any of them so no idea if they are any good.