Well, it seems that you will be in and around Tokyo from the 18th through the 22nd. Depending on when you catch your trains, you then will have 4 full days plus up to 2 half-days in and around Kyoto/Osaka. Remember, they are only a few minutes apart on the shinkansen (if you have a JR Rail Pass) or less than an hour on local trains.

My thought is that you will have time in Kyoto to do a full day trip to Osaka - you might want to stay into the evening to experience the vibrant night scene there - and perhaps another day trip to Nara or perhaps to Hikone to see the castle. That would still leave you 2 full days plus 2 half-days in Kyoto. Or, if you find you just haven't seen everything you want to see, just scrap one of the day trips and use that day for more of Kyoto. Everything is so close together and so easy to get to by train with a Rail Pass that changing plans as you go is very easy.

In case you haven't already done so, I'd recommend obtaining a good guidebook. There is so much to see in Kyoto and Tokyo that you will have to pick and choose what to spend your time on. You can also get a nice tourist guide for Kyoto at the Tourist Information Center on the 9th floor of the Kyoto Station building, along with a bus route map.