Transportation Questions for First-Time Travelers

We are three first-time travelers to the country in June and were wondering what would be the best ways to get around the country to our destinations. We plan to land in Haneda, go to Tokyo for 4 days, head to Kyoto for 5 (including a day trip to a village near Nagoya as well as a trip to the outer parts of Kyoto), Osaka for a day, Yokohama for a day, and back to Tokyo for 2 more.

I keep reading about the Kyoto bus system not being the best, the JR Pass not being worth it, and the weather being rainy (the least of which are an issue due to us being accustomed to tropical weather). What would be the best routes to take for getting ahead with transportation and is the JR Pass worth it?

by cptnsistermidnight

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