In february this year I had to shift my labrador from Bangalore to Orissa. And had a first time experience of travelling with a pet by Indian Railways. Here are some points to help other pet owners when they intent to.  
 
-- Visit the luggage booking counter 2 days before (if not atleast a day before) the journey and enquire about the trains that have the dog box and pet transportation option. There may be many trains going from and to your destination but not all have the dog boxes in them.
 
-- The booking counter normally books the pet a few hours before journey (in my case 9 hours before), so expect a second visit to the railways station before the final journey. Make sure you come well ahead of the booking time as there are only 1 or 2 dog boxes and there may be other pet owners. 
 
-- When booking make sure you have your Journey ticket on the same train with you. This is required at the time of the booking. Mandatory.
 
-- Have a travel fitness certificate from your vet. The booking person may not say this during booking but when you arrive with your pet they (may) ask for it. It happend in my case.
 
-- Have a sedative with you for your dog. Prefer the ones which are herbal and have no side effects. These pills lower the metabolic rate which reduces the urine and potty frequency of your dog.
 
-- The dog boxes are not clean, arrive early and pay some cash to the cleaners there to clean it for you.
 
-- Have a travel companion, believe me it helps.
 
-- Important : Every time the train engine head changes, you have to move your pet to the other end where the guard is stationed. This is a tedious work, specially if the train is very long and stations are crowded. I had to do this twice.
 
-- Give your mobile number to the guard in charge, ask him to call you (they won't, they will miss call) in case of anything. Take their number as well. Be ready to shell out some cash to them as well
 
-- Don't give too much water to your pet. This will increase chances of him urinating in the dog box. Its a very small, crampy place and can be unhygenic in such a case.
-- Feed him solid food, pedigree or any other dog food is the best option. Feed him just once within 24 hours. Don't over feed.
 
-- Visit him on stops if possible. During major stops if you find that the train is getting cleaned, pay a cleaner and get the dog box cleaned as well if its  long journey, it also makes it cool for him to stay inside specially during a summer season.