Just done the journey, a few observations/tips:
Take the lower berth, it is wider and only costs 100 baht more.
The buffet cart is limited so take your own munchies and bevvies.
The train arrives in Hat Yai at about 7am where it connects up with another and the beds are converted to seats.
There are money changers on the train offering close to the market rate (10 baht to the Ringgit).
You get to the border an hour later, off the train, exit Thailand, into Malaysia on the other platform, through customs (they will check your bags), then back on the same train.
The leg from Pedang Basar to Butterworth is a slow, dull 3-4 chilly hours on two carriages of the original train.
The Thai side of the journey is noisy, bumpy and rough, the Malay side has smooth and quiet rails.
Ignore the taxi mafia that want a grand and follow the signs to the ferry, it is 1.6 ringgit (16 baht) and takes about half hour.
Then you have a mele with the taxi scum when you arrive in GT!
There was a 2 hour delay at the border as we didn't have a locomotive for the onward journey.
18 hours later and we're in Georgetown which is nothing like I remember and bears more resemblance to Bangkok on first impressions. Full trip report to follow.