You should apply for your passport as soon as possible, especially if you are going to be in Japan for awhile. It can take a few months at least. I guess you can have it mailed to your parents if you'll be gone. You won't need a Visa if you're only going for 21 days.
As far as languages go, Spanish would probably be the easiest to learn but you may not be spending much time in Spain if you're going in February. I'd say French, German, and Italian are necessary. Just try to learn at least a little of the language of each country you want to visit. It's not as hard as you would think once you're immersed in their culture.
I'd say 60 Euros/day is a very good estimate. Your plane ticket will be under $1000 USD, most likely (depending where you're flying to and from). The Eurorail pass varies depending on the number of days. Their website is a bit complicated, but most guidebooks will spell it out for you in very simple terms.