I'm an Old Japan Hand (first went in 1977 as a student and have been back 13 times since), and I have never had any problems with safety.
There are plenty of good guidebooks available, and signs are bilingual (English-Japanese) in train and subway stations.
The Japan Rail Pass is a good deal if you are going to be making at least a round trip between Tokyo and Kyoto or an equivalent distance. Otherwise, you're better off buying individual tickets.
One of the great things about Japan is that you don't have to stay in an expensive hotel to enjoy safety and cleanliness. The average "business hotels" (mostly basic single rooms with private bath) are about $100 a night or less, depending on the city, and some include breakfast.
You also don't have to be afraid to eat in low-cost restaurants or drink the tap water, because the standards of sanitation are quite high.
Everyone under the age of about 65 has studied at least 3 years of English. This doesn't mean that they speak it--they've either forgotten it or are too scared--but almost everyone can read simple English written in block letters.
Every region has its own handicrafts, and they tend to come in both cheap and expensive versions. For example, Kyoto is famous for its brocades. You can spend thousands of dollars for a bolt of the finest kimono cloth or else you can spend about $20 for a coin purse and billfold set. Your guidebook will tell you what each region is famous for.
If you decide to visit Tokyo as well, then you'll see both traditional and modern Japan, but if you stay in Kyoto, be sure to go to Nara as well. That's the eighth century capital, about 30 minutes away by train, and it's even more peaceful than Kyoto and much more compact.
The best times to go to Japan are in the spring between March and mid-May and in the fall from October through early December. Winters aren't bad in Kyoto and Tokyo (dry, with highs of about 5°C--in the 40's Fahrenheit), but you won't see many plants. June is rainy and muggy, and July through September is hot, hot, hot, especially in Kyoto, which is surrounded by mountains on three sides.
If you're interested in Japan, start by buying a guidebook and reading up on it (or whichever country you decide to go to). I recommend the Insight Guides with their beautiful photography and excellent essays on the local culture as background reading for any country, followed by one of the standard guidebooks (Lonely Planet, Frommers, Rough Guide) for the nitty gritty details.