I think taking the train from Kuala Lumpur to Singapore would be ideal vs taking a plane. Its close enough to take a train and far enough it would be ridiculous if i chicken out and take a plane.
I found a wonderful website that talks about all sorts of train travel. Including the leg from KL to SIN i was looking for. Thank you man in seat 61. This was a lot of information that i found very useful :http://www.seat61.com/Malaysia.htm