What could cause Sarawak and Sabah to not be a part of Malaysia in the present day? Leaving the Malaysian Federation or not joining it at all in 1963 is one option, as is having a different colonial relationship with the UK- perhaps more white settlers (very unlikely though) or being important enough or dependent enough to not want independence in the 1960s (slightly more likely).
If they did not join the Malaysian Federation what would these two states look like? Would they be one state or two, maybe joining Brunei or even Singapore?