My trip report for KTMB first class from SIN to KUL a few years back:

http://www.flyertalk.com/forum/showthread.php?t=317727

I'm generally a train buff who among other things has spent 3 months Interrailing around Europe, but all things considered, I prefer the bus. The narrow gauge trains shake and rattle quite a bit, making it tough to sleep, and the early morning arrival is pretty brutal.

As for tickets, you'll get charged in SGD (=double the price) if you book any trip out of Singapore. I thus booked the cheapest possible SIN-somewhere trip in cheapo class (in SGD) plus a JB-KL first class sleeper (in ringgit), which saved a fair chunk of cash with minimal inconvenience (because you have to get out of the train with all your stuff at the border anyway).