I've also done this trip in both directions in March 2006 (SIN-KUL overnight, then actually onto Penang and back). I bought my ticket for SIN-KUL at the train station in SIN. Probably more money, but I liked the flexibility and didn't have internet access at the time in SIN to make the purchase online. The ride was fine. Bring some food if you're hungry. Otherwise, you can buy some stuff they sell on board, but it didn't look too appealing to me at the time. I'm sure it was fine, just didn't look too appealing.

You probably won't get too much sleep on the 2nd class sleeper depending on how tall you are. I'm 5'7" or 5'8" on a good day and I couldn't lay out flat without my knees bent. So if that's a concern, you may wish to pay for a higher class cabin or buy a seat and pretend it's a flight in Y. Also, while there are curtains you can close, they tend to leave the lights on in the train compartment and light can seep through. Also, since people are constantly getting on and off the train, at stops people will sometimes brush by your curtain and pull it a little, etc. Nothing that is abnormal to train travel around the world, but perhaps a bit of a nuisance to someone who hasn't done much overnight train travel.

On the return, since it was daytime, I took the 2nd class seats. It was very comfortable and the ride was beautiful. Looking at the countryside from a train window is very therapeutic and a great way to be introspective, if you're into that kind of thing.

It sounds like there are other experts on this route, but if you want to ask me anything further, please PM as I might not catch this thread again.