Hi,
I hope I could shed some light on the places to visit while you're in Malaysia for 2-3 weeks:

Kuala Lumpur(2-3 days)
Taman Negara (3-4 days)
Perhentian Island (3-4 days)
Penang (2 days)
Kuala Lumpur (2 days; including a day trip to Melaka)
Sandakan(3-4 days)
Tawau (2-3 days)
Kota Kinabalu (3 days)

*** optional ***
Kuching (3 days)
***optional***

Kuala Lumpur (1 day)

Off to next destination.


//Kamel