If you fly into Osaka KIX and out of Tokyo NRT, purchasing a JR Pass makes no sense.
-KIX to Osaka proper by bus: 880 to 1,300 yen
http://www.kansai-airport.or.jp/en/access/bus/index.html-By train (Nankai) to Namba: Limited express 'rapi:t'; 1,390 yen, express; 890 yen
-Osaka to Kyoto by train:
JR: 540 yen
Hankyu: 390 yen
-Kyoto to Tokyo by Shinkansen:
13,220 yen on Hikari, 300 yen more on Nozomi
-Tokyo to Narita by train:
JR: 2,940 yen on Narita Express
Keisei: 1,920 yen on Skyliner, 1,000 yen on limited express
By the way, if you intend to travel between Kansai Airport and Shin-Osaka or Kyoto by JR limited express Haruka, purchasing the JR West Kansai one day pass for 2,000 yen is a nice idea. It allows you to take the unreserved section of that train between the segments above. You can purchase as many vouchers as you like before you come to Japan.
http://www.westjr.co.jp/english/travel/jrp/index.htmlBreakdown of JR individual tickets just in case you make a round trip:
KIX to Osaka: 2,000 yen (JR West Pass)
Osaka to Kyoto: 540 yen
Kyoto to Tokyo: 13,220 yen
Transport in Tokyo per day: 500 x ? days =
Tokyo to KIX: 15,630 yen
Total: 31,390, as opposed to 28,300 yen pass
You could optimize the pass if you travel to Nikko from Tokyo, or to Hiroshima from Kyoto or Osaka.