1- Yes, absolutely. The earliest shinkansen departs at 6:14 from Kyoto and arrives at 9:00 in Tokyo. Add in the ~40 minutes to get to Miraikan and you should be there at around 10:00.
To get to Narita on time (about 2 hours early), you’ll have to leave at about 17:30, leaving you with a more than enough 7 hours to visit.
2- This is completely subjective, but if you enjoy technology and science, go for it. I found the exibits very interesting. You might also want to visit the nearby Gundam Front Tokyo
3- Yes, there are plenty of coin lockers in Tokyo station. These will cost you up to 500 yen depending on the size you choose.
Credit:stackoverflow.com‘