You need to done your Visa First....most important.

Because you want to go Universal Studio....so you need travel between Tokyo and Osaka....you need JR Rail Pass also. 

How to get Visa and Jr Rail Pass....I won't told you here.....You must do the Homework.....

After done this 2 ......Then you can Post your Trip Plan  here.  From 1st day until last day..

We will do the adjustment for you to get the best journey in most time saving.
I sense your Trip going to used more than RM10k

Muslim food is actually quite easy to find in Tokyo. Go to Shinokubo (新大久保）and you will find lots of halal shops selling uncooked halal beef, chicken, mutton in case you are thinking of cooking over here. And there are plenty of halal indian restaurants you can go to. Halal Malaysian restaurants too.

you can try reading these :

http://forum.lowyat.net/topic/2034076/+100

http://forum.lowyat.net/topic/2034076/+140

There's a list of food that we can't eat and list of halal restaurants   Hope this is useful for you. Enjoy!

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Added on February 16, 2012, 3:41 pm

Going by Air Asia?

If Yes.

You Lost one day at Flight already and Lost another Day back to Malaysia.

6 Days trip means you actually in Japan just 4 days ....plan wisely.

You can set 2 day at Tokyo , half day at Kyoto , 1 and half Day at Osaka .....back to Tokyo for another 1 day. Then Back Malaysia

Air Asia to Japan biggest weakness are arrive Haneda around 10:30Pm - 11Pm. It was so late. The Tokyo Public transport are going to stop operation. (you will miss the last train if you didn't do much homework)

How to go Tokyo City if I arrive Late?

Please PM a guy call Stimix......he will teach you.

Still Most important thing are JR Rail Pass......