Considerations
Some things to keep in mind when planning your trip:
Wear a Helmet!
You don't wear a helmet because you'll need it every time. You wear one because, if you ever DO need it, you will really, REALLY need it. After a decade of wearing a helmet and never having a serious accident, one day I whacked my head on the pavement with enough force to convince me that I would have been seriously injured without the helmet. And the accident occurred on the way home from the store near my apartment - exactly the kind of situation in which I would not have been wearing a helmet unless I made it a rule to always do so.
The moral of the story is clear. ALWAYS WEAR A HELMET. Before you get on the bike, make sure the helmet's on you.
Plan Ahead!
The more planning and checking of options that you do in advance, the less you'll have the do on the fly... and the less likely you are to get yourself in trouble (see the Safety section for more on this). Planning ahead will, for example, make sure you have a room reservation on the 3rd and 4th of May, usually the crunch days of the Golden Week vacation when everyone in the country is on the move and virtually every hotel, ryokan and minshuku in the country is booked solid.
Be Prepared!
A flat tire can either be a fifteen-minute inconvenience or a complete disaster, depending on whether or not you're prepared. If you don't know how to change a tire, learn now - and practice making minor adjustments on your bike as well. There's nothing quite as dispiriting as fiddling with unfamiliar tools while the sun is going down on a lonely mountain road in early winter...
By itself, a patch kit is not enough - remember to take a portable pump as well, just in case there's no service station nearby when your tire decides to blow. Also take some simple tools; a bike shop can help you get what you need. In my backpack, I carry a small case with all of the things I've ever needed on the road: patch kit, simple tools, spare patches, spare cables, spare tire tubes, spare headlamp bulbs and batteries, tiny container of lubricant -- and, if it’s a long trip, also including a spare chain, spokes (you can get by without a few of these, though), spare quick-release rods that pass through the hubs (break one of these - and, yes, I have - and your wheel is non-functional!) and even a tiny respirator if I know I’m going to be cycling on highways clogged with cars and exhaust fumes, like the truck-and-tunnel-laden road to Norikura and Kamikochi in the Japan Alps. (Also, use illuminated lights on both front and rear when cycling through tunnels — and see our special report on Japan Alps Tunnels.) All of this is not nearly as heavy as you might expect, and the peace of mind is priceless.
Nevertheless, for all nonessentials, you should make an effort to...
Lighten Up!
Carrying the bike bag and tools will make you want to keep your other gear light. This is easy during the warm months. My standard summer kit fits in a single backpack: cycling gloves (great for reducing hand fatigue on those long trips!) bike tools, pump, map, headlight and taillight and spare batteries, sunscreen, hat, light windbreaker, bathing suit, change of clothes, and of course the rolled-up bikebag. Winter adds a couple of extra layers, warmer gloves and a woolen cap for those cold, COLD mornings.
Neatness Counts!
Do your hands a favor and take along a pair of cheap, lightweight gloves (I use disposable vinyl ones) in a plastic bag for use when packing and unpacking the bike. You'll see the value of this after your first greasy packing job.
Drink Up!
Make sure you get enough water. Along most roads there are soft drink vending machines almost everywhere you look. The places to be careful are toll roads and those tiny mountain paths that are most ideal for cycling; you can go for miles without finding anything to drink. (Hokkaido also deserves special mention in this respect: even fairly major roads have not even a single vending machine for virtually their entire length!) Your bike should have a bottle cage already on it; if it doesn't, get one before you leave. Note that in Japan the only bottle cages that are widely available seem to be designed for the ubiquitous 500 ml PET bottles. The ones that were previously available were wider and the perfect size to scrunch in one of the ubiquitous 1.5-liter PET bottles that you could buy in any convenience store; at best, the smaller cages will accommodate only a 1 liter PET bottle, which to my mind is still too little for cycling uphill or on very isolated roads. Moreover, those 1.5 liter round bottles are now less ubiquitous: the stores now seem to stock square-shaped 2 liter bottles that are more refrigerator-stackable but completely unsuitable for bicycle use. (Since it’s a larger quantity for a lower price, it’s hard to complain.) My advice would be to find a wider bottle cage before you go and buy one 1.5 liter PET bottle and refill it with water or the widely available 2 liter square bottles. Japan has several popular brands of sports drinks, primarily "Aquarius" and the awfully named "Pocari Sweat." Some convenience stores (like Seico Mart in Hokkaido) now offer their own brand of sports drink at a lower price.
Cover Up!
Even if you never burn and aren't scared of skin cancer, it doesn't hurt to wear sunscreen. Don't underestimate the sun in summer, or anytime for that matter. Wearing a long-sleeved cycling jersey made of one of those miracle fabrics that breathe amazingly well will help you cut down on sunscreen costs (it's expensive here). Sun protection should extend to your eyes as well; sunglasses are highly recommended, particularly to cut the glare from the bright summer sun. If you wear glasses already, you can get a special “UV cut” coating put on the lenses.
Don't Wind Up in a Ditch!
You won't have to cycle long before you notice the open concrete ditches that are present on both sides of most Japanese roads. These rain-drains are usually uncovered and often quite deep (sometimes nearly a meter), and while they present no danger to automobile tires, they are true death-traps for bicyclists. Most cyclists in Japan get used to their presence and avoid them almost unconsciously; you should develop the same knack as soon as possible. Be sure to take it slow on curves so you don't over- or undercorrect, or you could find yourself in real trouble; entering one of these ditches with a tire at high speed will surely result in serious injury or at least serious bike damage.
...and, above all...
Take it Easy!
Remember that cycle-touring is different from racing. You're not trying to win the race, you're trying to make it to the finish line alive. Go at your own pace - and by that I mean, don't try to over-extend yourself. Cyclists who have more experience or are in better shape than you are going to make it over the hill first in any case; don't feel pressured to try to compete with them and exhaust yourself early on. A little practice will tell you the difference between being tired and being exhausted; you'll soon know how far you can push yourself and still stay on the bike till day's end. Most importantly, remember that "Arrive Alive" applies to cycling as well as driving.