I've got a 10-day rental reserved for Christmas from Nissan for ~¥44k, so don't think what you're getting is unreasonable. Note that this price includes only the lowest level of insurance (I think ¥250,000 deductible for damage).

I've done this once after picking up the car - instead of returning to the pick-up location, I wanted to extend the rental and return to a different location. My experience has been that returning to a different location adds a lot to the cost (my experience has been about ¥50k). In my case, since my rental was due and I was in the area, I drove back to the rental office and asked about different pricing in person, but I suppose you can do the same over the phone.

If you want to change your plans before picking up but after making the reservation, I would just make a new reservation and cancel the old one. I don't think any direct rental I've made in Japan asked for a credit card. But still, definitely review your reservation to see what the cancelation terms are.