My parents lived in Malaysia for years, and I lived there briefly. A large segment of the population is muslim, and generally has the political power in the country - as opposed to the chinese population that has most of the financial power.
It's a pretty nice civilized place, actually, and we never had any trouble at all while we lived there - but that was almost 20 years ago, so I suppose things might have changed. But, we were some of the only white people living in an area. Of the local town with a population of about 60000, there were less than 10 white folks, and we never felt any hostility or danger. I trained with a local TaeKwonDo club in town at night, for example, and never worried about anything.
Kuala Lumpur is nice, and you can drive from Johore Baru right over a bridge to Singapore, which is really nice too. If you have time to relax, there are some beautiful resorts, beaches and islands on either coast.