Coach ferries were typically used only on MG lines.
On the BG lines passengers had to get down the train and use a ferry to cross the rivers.
The precursor of the present day Kalka mail only started in 1891 after the Delhi-Panipat-Ambala route was opened. Prior to that there was only one mail train from Calcutta to Allahabad which carried through carriages to Lahore and Bombay. At Allahabad, these through coaches were attached to different trains to continue their journey to Lahore and Bombay.
The...
more... statement that the Kalka mail started in 1866 was put forward by railfans and IR just started publicizing it without any research or verification. I had filed an RTI asking for documents to support this claim, and ER replied back telling me that they do not have any such records. (I had shared the RTI reply a couple of years ago on this site).