I'm now taking the exact trip descibed in the first msg of this thread. It's a 2-1/2 week trip. I'm in Georgetown, on Penang Island, Malaysia.
People here are as friendly as any I've met all over. I sense zero danger to a Western traveller on the west coast of Malysia. The East coast presents several problems:
monsoons, tougher travel facilities, and possibly more fundamental religous feelings.
I think the same fares are available now, within a few dollars. I liked the break in Hawaii. If you get to Tokyo early (I did) plenty of time for a trip to Narita City to see the temple and gardens, and have lunch.