I think you had bigger bags than usual, my impression was it was Y500 per CALENDAR day (as you noted, drop on Monday, pick up Tuesday, it's 2 days). It still is pretty pricey. It's also a hassle to take it between terminals.

I'd be tempted to carry it into Tokyo, and use the money saved on a locker to take a taxi to/from the train station if you take the train in. If you take the airport limousine to your hotel, then there is no extra hassle although there is a moderate extra charge for each piece over 2, I believe.