I spent about ten days in Southeast Asia about a year ago...spent three days in Singapore, three in Cambodia, and three in Kuala Lumpur. Best ten days of my life.
We had a choice of going anywhere between Singapore and KL, but we decided Cambodia over Thailand and the rest of Indochina because it was the most exotic and the temples were amazing.
Here is a GREAT tour guide company for Indochina. It's more than the average tour guide. I still correspond to mine via e-mail!
As for KL, I would definitely go to the Batu Caves... it's less than an hour outside KL. The KL Tower is a must-see, but the Petronas Towers are not worth going up...they will only take you half-way up (44th floor).
We had an extra day in KL and the hotel staff told us to visit some sort of national park 4 hours outside KL, but we didn't have the time. It sounds like you might, though. I'll try and find some info on it if I can. I believe KL also has a great zoo worth seeing. Oh, and I'd make a visit to the National Mosque or the Palace. There's also an Islamic Art Museum that sounded really interesting, but my dad didn't want to go.
You can also get a cheap flight from KL to Singapore... it's only about a forty minute flight. I can also tell you tons of places to see there.
And if you're looking for hotels, I recommend the Shangri-La in Kuala Lumpur. I also have many more hotel recommendations.
