If you aren't going for a year or so, start using a currency update service, such as at
XE - The World's Favorite Currency and Foreign Exchange Site. Keep an eye on the way the currency moves and spend a few months getting to know its trends, and it's regular highs and lows. For example, Sterling to Yen, the average range is 110 - 145 yen to the pound, but has spiked due to unusual circumstances at a whopping 180 yen to the pound late last year.
Then when you come to buy your yen you know whether the rate your getting is acceptable or whether you should wait for it to change, and you'll know roughly how long to wait for that change.
You also need to keep an eye on the news in Japan - unexpected problems can prove remarkably beneficial in buying and selling currency. Events which cause a momentary downward blip in the value of yen can help you out tremendously if they coincide with an event which causes an upward blip in the value of your own currency.
Remember also that rates on currency sites are BETTER than those you will actually get. They are average rates calculated on MASSIVE transactions with bulk-buy discounts. You will then need to shop around for the best rate that you can actually get.
And, yes. Take cash to Japan. It's pretty safe to do so (but, frankly, I've not even been mugged in my own country, let alone any other). Just don't be dumb enough to carry 100,000 yen in your wallet. I tend to transfer a daily amount to my wallet every morning before I go out, then stash the rest somewhere safe. That way when I'm rooting around to pay for stuff I've got about 10,000 yen in there and even if someone does snatch it I'm not cashless for the rest of the trip. This is just common sense no matter what currency you're carrying.