Trains are not commonly used in Malaysia as a way to get around. I'd imagine that if you can find one to take it would be very clean and well run. Personally I'd rather take a bus...of which they have many of very high quality running frequently. It takes about 4 hours from KL to Singapore and the cost will vary depending on the style of bus you take...but will be very reasonable no matter what.
Basically the bus system in Malaysia is much more developed than the train system.