Not missing much not going to KL except for the Petronas Towers. One day would be enough.
Wouldn't worry too much about the there and Bali/Indonesia being mostly Muslim oriented. Many westerners in those places and most locals are quite open and friendly. Not radical like the Arab world where women are covered up and all the reported violence is taking place.
Although Kuta is the popular beach scene in Bali, it is also the most 'rough' area. Lots of backpacking Aussies and local drug touts in the open harassing westerners/tourists to buy stuff. Nusa Dua and Ubud are the areas to be in Bali.
Would definitely try to fit in Boracay (Philippines) and Phuket & Koh Samui (Thailand) to the list.