Ifm going to first say I might have put too much of my desires into the itinerary. This is somewhat my plan for next year, but I am going slower. You never mentioned Takayama in your original post, and I steered you to it, as an alternative due to construction.
Next year, I plan to take the highway bus to Takayama on May 13th, the day before the festival. My plan is to stay a week. I plan to also do the cablecar, and the Alpine Route, as well as attend a drum festival in HidaFurukawa on the 18th & 19th. It is 15-20 minutes away from Takayama.
I plan to take the highway bus to Kyoto, and spend time there.
I was then going to get the 5-day Kintetsu pass, and visit Mount Yoshino, Nara, Osaka Namba, Iga Ueno to see the Ninja Museum, before ending up at Ise.
After that, I was getting the Ise-Kumano-Wakayama pass for five days, and heading towards KiiKatsurra.
So... I gave you part of my idea. It is sound, and will cost less than a 7-day JR pass. Takayama also filled in as an good alternative to Hakone, or, the Fuji Five Lakes. I have traveled to Japan several times, so I have figured out how to get around some places.
I have also found that the JR pass is not the end-all golden ticket for traveling around Japan. Local transportation is usually not done by JR pass, but there are exceptions. Municipal transportation, like busses and subways, are not covered. At most tourist attractions, some independent local vendor has built something, and charges you.
So... If you were going to Mount Yoshino, you were going to need a Kintetsu two day pass, or better, because JR doesnft go there. I still think I gave you a good framework for your trip.
Ok... that said, I wanted to mention having a larger Kintetsu pass, because it gives you buses in Osaka for any additional day spent there, and the Ninja Museum at Iga Ueno. If, while reading this post, you stopped and went, gWhoa... a NINJA MUSEUM!!! I gotta go there!h, get the bigger Kintetsu pass, add another day in Nara, and take a day trip there. The pass also allows you to use busses in Osaka, for days after you get to Osaka Namba, so it has additional value. It could also be used to end up in Nagoya, so that the Shinkansen Bullet train ticket back to Tokyo is less.
Once again, good luck, in planning your vacation.