I would suggest the 7-day Rail Pass for the Tokyo-Kyoto-Tokyo part of the trip as jib71 mentioned. It will cover that round-trip and other rail travel during the 7 days. I would also recommend adding another day trip from Kyoto to Himeji (for the spectacular feudal castle) or even Hiroshima. Both can be done as day trips from Kyoto. If you add at least one of those trips the Rail Pass will definitely be worth the expense.