6 days in Japan itenerary

Oh, and of course, which JR pass should we get to cover all of our bases? I think the 7-day JR pass should work, right?

A 7 day JR Pass would not be cost effective for your itinerary. You'd need to return to Tokyo, or extend your trip somewhere significantly farther, like going to Hiroshima and back to Osaka.
In Tokyo a few of the best places to see are the Tsukiji Fish Market, plus the site that every last tourist goes to see, the Sensoji Temple. If you are in Tokyo on a Sunday afternoon, be sure to go visit Harajuku to see the youth with their wild fashions. Meiji Shrine and Yoyogi Park are next to it and well worth seeing also. And be sure not to miss the Shibuya Hachiko intersection especially on a weekend when it looks like half the city is crossing the street at once.
In Kyoto you could spend weeks there and not see everything. The three best sights though are the Kinkakuji Temple, Kiyomizudera Temple, and Fushimi Inari Shrine. Fushimi is the most time consuming; you could spend a couple of hours to over half a day if you want to romp over all the trails.
One of the first things you should do when arriving at Kyoto Stn is go to the 2nd floor tourist info office. There are many useful free maps and other help.
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are wonderful. During the day, consider going to see Nara. Along with Kyoto it is a former capital and one of the crown jewels of Japanese culture. The Todaiji Great Buddha is a must-see place and there are many other good places in Nara Park there as well.

Best of luck.