To get the most out of your transport pass, you need to study its mechanics and compare other travel options against it to see if it works for you.
The secret is that there's a lot of wiggle room budgeting for food. Yes, you can drop up to 15,000 yen per person for a high-end kaiseki meal or a deluxe Matsuzaka beef dinner. It's also very possible to spend as little as 300-700 yen per meal, without suffering from the great drop in quality you might expect from such a big price difference. The Japanese even have a term for such cheap-but-good eats: Grade B Gourmet.
Unless you're traveling to Japan on a tour that takes care of all your transportation, you'll likely have to take Japanese public transport at some point. The good news is that Japan has one of the world's best-developed commuter networks: wide-reaching, convenient, and incredibly reliable.