hi hun..
I travelled to KL when I was abt 15 weeks. no problems at all. you dont need to go to 5 star hotels. restaurants are ok. if you are not used to hawker style food, try to avoid it. I had had it before and ate it anyway. having said that I'm M'sian born.
Are you going to be in teh city only? You dont need any vaccination etc. You dont need to brush your teeth with bottled water
KL - the food is to die for!! and restaurants etc are all very good. enjoy all the food, but as the same here, avoid shellfish etc.
Flight's no problem. who are you flying with? I flew with Malaysia Airlines and when i told them I was pg, the crew were fantastic. even came up to me in the middle of teh night(i couldnt sleep) and ask if i need a hot drink etc. Do get some flight socks tho.

I assume with 5.5 hrs flight you must be on teh west coast. it's not a long flight so you'll be fine.

I cant say how jealous I am that you are going! (Actually I'm going back late Aug) I so love the food there. It will be very warm, so dress lightly.