Hi. Welcome to Tokyo! Good thing about Meguro... it's near the Malaysian Embassy.

Anyway, reality check - 50,000 yen for room + utilities etc will be very hard to get if you want to stay in Meguro. If you do find a place that fits that budget, you'll be staying in a pretty old building or a really tiny room. Getting a room only (eg back in Malaysia style) rather than your own place is very uncommon here unless you're looking at Guest Houses. I've not stayed in guest houses before so I cannot offer you my insights on it.

Here's a couple of websites for you to get a grasp of what the usual rentals are like in Japan (1K, 1DK, 2DK etc...) and the estimated costs.
1. http://www.chintai-k.com/c1a_13_110/ (This is already selected for Meguro).
2. Homes.co.jp (This is already selected for JR Meguro).
3. http://rent.realestate.yahoo.co.jp/03/

Use Google Translate to translate the site if you're not familiar with Jap language.

Word of advice:
Renting a place on your own will be very hard due to the fact that you're a foreigner and you're unable to communicate in Japanese. While it is not a must, most of the time you'll find that you'll need a guarantor in order to seal the deal. Also, will you be here long term/short term? Most rental contracts are for a minimum of 2 years and this is something you need to look into. Then you'll have the extra cost of the security deposit, 1-2 months advance payment, agent fees to think about for your first time payment.

I think it might be best to engage the help of your Uni dept or someone whom you can get assistance from there. They might be able to help cut the red tape that's involved to get you a place.

35,000 JPY for food per month is really low... you're looking at 1,000+ JPY per day for the ENTIRE month. I don't know about you; but it's Tokyo and with that budget do you mean you do not plan to eat out/socialize etc???