Do it.. Easy... We have done it many times before.
When you ring up to book your ticket.. make sure you get a first class sleeper if you will go with the bike.
You don't want to be in noisy unconfortable 2nd class...
You must go and pay for the ticket with in 2 days time and quote the reference numbers.. Let them know you will take a bike so they don't book you on a train with out the facility to carry bikes
or
Book 3rd class.. 200 baht or there abouts. Then take an Air Asia / Nok Air flight to CM.
If you do this.. Do not tell them you will not accompany the bike.. You are suppose to.
We have done this many times and rolled up 3 or 4 hours after the train has arrived and the bikes are locked up and someone watching them.. 100 baht tip and done.
On average when taking the Ninja or the KLX it has always been around 1200 baht from Bangkok for the bike.. They are corrupt at this station and once you pay you get the receipt which is about 150 baht or so less than the amount you paid.. What can you do? Nothing, if you want to make sure your bike makes it in one piece.. Funny thing is it is cheaper coming back usually even with out the corruption..
Never had the corruption thing coming back to BKK from CM / Udon or Ubon.. They all want the 100 baht tip for lifting the bike off and on of course.. which is fine. That is usually shared between the 3 or 4 of them lifting it off and on.. don't pay it to the guy you bought the ticket from.. i did this once and saw he only gave them 60 baht and kept 40 baht for himself.. Pay it directly to the guys lifting the bike off and on.
You are suppose to get the bike there 1 or 2 hours before.. we took it earlier once in BKK and they complained.. Told them I had to get jabs for Laos at the hospital and they agreed.. (didn't really need jabs).
Suggest you protect the tank with some bubble wrap. My friend had a nice dent in his Ninja tank..
They tend to stack boxes and other things on top and you can't always see as cargo may join at the other stops..
A lot of things are not so secure in the back of the train and they use rope that is tied together to secure the bikes to the side of the carriage.
Hope this helps.
Cheers
Brian