OK, so you have 3 destinations that are must dos. If you were just 2 or 3 people it's a lot easier to move to a location for 1 or 2 nights, but unless you all pack light or plan to do a lot of takyuubinning, I think doing single nights places would be hard. I still might takyuubin from Tokyo to KIX and then travel with just small overnight bags from Tokyo onwards to Osaka. I would stay in Osaka the night before you go, but honestly, the Osaka aquarium is not really any nicer than the ones in SF.
I've never hired a private guide, but I've also never traveled in a big group. If you can afford it, a private guide might be helpful just for juggling transport to locations. I would be leery of joining on an organized tour though, just because sometimes they spend more time at a location you want to leave and less in one you want to see more of. This can particularly be an issue with kids. If you are hiring a guide you really need to decide where you want to go. I wouldn't hire one for Tokyo. I would instead split up based on interests like museums vs. shopping vs. whatever your interests are...
If the grandparents are willing to split up, that works really nice, since it is a way to get in more places. I like Nikko but you are trying to get a lot in already so having the grandparents go there instead of TDR makes sense.
Since for Kyoto you only list Nara as a must do and for Tokyo you only list Sea and Kawaguchiko I would probably do:
April 7 Kyoto (night Kyoto)
April 8 Nara (night Kyoto)
April 9 Kyoto (night Kyoto)
April 10 Kyoto (night Kyoto)
April 12 Kyoto/Hiroshima (night Miyajima) Pass day 1
April 13 Hiroshima/Tokyo (night Tokyo) Pass day 2
April 14 Tokyo (night Tokyo) Pass Day 3
April 15 Fuji 5 Lakes (night Tokyo) Pass day 4
April 16 Disney Sea (night Tokyo) Pass day 5
April 17 Tokyo/Kanazawa ( night Kanazawa) Pass day 6
April 18 Kanazawa/Osaka(night Osaka) Pass Day 7
April 20 (fly from Osaka)
I would see if a 1 week pass makes sense, it more than likely does. I put Fuji 5 Lakes towards the end of your Tokyo time in the hopes the shibazakura are in bloom. All the sights in the area are open on Monday except the MagLev exhibition as well. If you change Fuji 5 Lakes to the 14th you risk Sunday crowds because it should be around sakura season and Sundays are when people have off. I picked the 16th for Sea because it is currently forecast to be a low crowd day.:
http://www15.plala.or.jp/gcap/disney/I would really try to go on a light blue day because TDR can just be so crowded. I went on a light orange day and it was just amazingly unpleasant. And yes I have been to the US parks.
If you discover more things you must do in Tokyo, I would cut Kanazawa, and the grandparents could always do it as a day trip. If you're already going to Kyoto I don't think Meiji Jingu or Sensoji are that interesting. Do be warned, kids tend to get temple fatigue. Kyoto has a great monkey park, though the climb to the top of the hill is long and steep. I've also been to the Toei Movie park when I needed a break. I bought my child a goshuin, which we collect stamps for to help make a memorable souvenir. I also found giving my child their own camera to take their own pictures made visiting gardens, temples and shrines a lot more interesting for her.
I mean Akihabara could have changed since I was last there. Previously it was all electronic stores and Otaku stores. Some of the figures in the Otaku stores are just cute, some are just posed sexily, and some are things I wish I could bleach from my memory and are not things I want my kid seeing. It's also just very bright and not somewhere I would personally want to stay. Ochanomizu and Kanda which are super close on a map but are quite different seem to have more hotels than Akihabara itself, are you sure you are in Akihabara and not Kanda or Ochanomizu? When you say 4 adults, do you mean you-spouse-2 kids, or do you mean 4 adults, you-spouse-2kids-grandparents?? Finding a room that can hold 6 occupants is really hard in Tokyo and you really need to check room sizes because a lot of places have tiny rooms and the twin beds in most twin rooms are both between the size of a US twin and a US double, which can be hard for two adults to share. If you have to stay in a luxury hotel to get two actual queen beds.
What age a hotel considers a child as an adult occupant varies by hotel. Some consider any child over 5 as an adult occupant. I notice it a lot, because I brought my child at 5, 6, and 7. There are plenty of hotels that would not count your 2 children as adult occupants. It just might take some looking.
Many hotels don't open up for reservations until 5-6 months before particular dates, so oddly enough in a month there will be even more potential room options.