Japan is more affordable than its reputation suggests. Budget travelers can get by on $50-70 per day by eating at convenience stores and ramen shops, staying in hostels or capsule hotels, and using IC cards for trains.
A mid-range budget of $120-180/day covers business hotels, sit-down restaurant meals, and major attractions. The JR Pass is worth it if you plan to travel between multiple cities by Shinkansen. Museum entry fees are generally modest at $5-15.