I'm doing a semi-last-minute trip this weekend.
1. Flying into NRT Saturday morning, staying 2 days in Tokyo
2. Then going to Kyoto Monday and staying 'till Wednesday night there
3. Flying from KIX Wednesday night.

I'm staying not far from Ueno Station in Tokyo.

What is the best combination of tickets to cover the ride from NRT, transport around Tokyo for +/- 48 hours, Shinkansen tickets, and Kyoto-KIX train?
From what I gather, there is no way at this point for me to get an advance-price discount on the Shinkansen. Is this correct?

I did not buy a railpass.

Thanks!

Edit: Cost is a concern, so if there's a cheaper way to get around that would be good to know. I prefer trains over buses.