Yeah, my guess is that JL F JFK-NRT is your best bet under the circumstances, followed by other JF F options if that routing proves unavailable. And I'm sure it will be very fine!

In a related time-saving and miles-saving mode if those are priorities, and as a fallback, you could also consider AA (!!!) in F from the USA to NRT, if it offers the 777W with the new F seats on a given route. It won't be the same cultural experience and the service likely won't be as good, but it will get you there with a nice hard product. But based on my own brief inquiries and the post above, I'd think you'll be able to snare two JL F seats.

A few more thoughts:

1. In exploring award space, see if HND (Haneeda) is available. I've never been through there, but it's the "other" Tokyo airport and is actually much closer to town. Some major carriers have started flying there in recent years.
2. Yet another variation on the theme re award space is to see if you could fly into or out of other major Japanese airports such as Nagoya (??) and Osaka for your trip, since they might be closer to where you'll start or end up in Japan. In planning our own wonderful trip, for example, I hadn't focused on the fact that Kyoto is much closer to Osaka than Tokyo, so wasted some time traveling back to Tokyo when flying out of the country.
3. Have you yet gotten and used the Hyatt Visa card that offers two free nights at any Hyatt in the world if space is available (which it generally is, if you book sufficiently far in advance)? Between you and your spouse, you could have four free nights at the Park Hyatt Tokyo, which would save you the conversion of some Chase Ultimate Reward points (which could in turn help open up the possibility of those SQ 380 F suites).
4. The PHT really is a unique hotel and memorable experience, by the way. As you may know, it's not as well situated as the Grand Hyatt, but getting around Tokyo is manageable from there anyway and we're glad we stayed at the PHT. Plus it is perhaps a 20 minute walk from a very nice large park (sorry I can't recall the name, but a map or the PHT can direct you there) that shares some green space with a a large temple area. And roughly on the other side of the park from where the PHT is, there is a major shopping street (that I believe is well known enough that the PHT will know about it) that becomes much more interesting once you branch off of it to the smaller side streets nearby, which have smaller shops, cafes, etc.
5. I've read great reports about the Hyatt Kyoto, so wouldn't discourage you from going there. But if you're looking to save Chase UR points/Hyatt points and if you have some SPG points to burn, one alternative to consider is the Westin Kyoto. It is a big, somewhat westernized hotel that lacks the charm and sophistication that I'd imagine the Hyatt and other properties have. But we found it to be fine (it helped that we lucked out with a rare suite upgrade due to my SPG Platinum status, though we would have liked it anyway) and really liked it's location: walking distance to what we considered the best and prettiest part of Kyoto, the Philosopher's Path that offers an easy stroll through nearby hills. The PP offers a full day of strolling to temples, manicured gardens, and small handicrafts and clothes shops and cute restaurants, and is less crowded than the center of town. Also near some hiking trails if you're so inclined, though we didn't explore those.
6. In a related experience-maximizing vein, I believe Hyatt still offers the Diamond status test run (or whatever it's called, exactly) for 90 days (???). If you time that right with your trip, the Diamond status would get you complimentary breakfasts, room upgrades and perhaps other perks on your trip. We did that for our stay at the PHT (combining it with the aforementioned four free Hyatt nights); it made a memorable stay even more so, including providing us with a wonderful breakfast that otherwise would have cost a fortune! More information at whether this Diamond status deal is still available and how it works (including whether you can still couple it with a free nights stay) at the Hyatt forum.
7. Other unsolicited thoughts: a) The bullet trains are fun and impressive. b) the manicured gardens are incredible! c) We were very underwhelmed by the ryokan (traditional Japanese guest inn) experience, but that could have been because we picked a poor (though expensive!) one; if you do decide to shell out for one, do some research and book far in advance. d) I'd highly recommend the "Haunted Tokyo Tour" walking tour we took with an American expat woman who's lived in Japan for many years: http://www.hauntedtokyotours.com/ Despite the way it's billed at the website as "ghost walks", it is more of an explanation of Japan's spiritual life and exploration of some Tokyo back streets and neighborhoods, which are much more interesting that its main avenues.

As you can see, I can really wax enthusiastic about Japan! In addition to all of the above, the day to day way in which the culture operates is fascinating and impressive. Have a great trip!

Whoops - I should know that since I just booked one...

Was thinking of the pre-deval UA ticket I have booked on NH F for the return :D

We got our flights to Tokyo booked on JAL first class from L.A. to Tokyo (Narita) and are ecstatic about it! Thanks so much for everyone's help!!!

Thunderroad, we are staying at the Westin Kyoto and flying back out of Osaka purely based on you thoughts, so thanks again!

Right now we are thinking that we will do 5 nights in Tokyo (Park Hyatt), 5 nights in the Westin Kyoto (with a day trip elsewehere or two), and two nights in Osaka at the Interccontinental. It looks like JAL from Osaka-Tokyo-L.A. is probably our best way to get back home (with a connection L.A. to Nashville to finish it off)?

I have used several of your suggestions and would LOVE any additional thoughts, ideas, corrections, recomendadtions, etc.

Thanks again!

My pleasure, Cubswin. A few more thoughts:

1. When are you going? That could affect some advice you could get here or elsewhere.
2. Also, what is your status at the hotels where you'll be staying? That could affect the advice you get re your hotels. You might want to include that in your FT ID information that goes with every post.
3. Now that you've nailed down the basic hotel/airline choices, you might pose specific questions in the Japan Forum here and at Tripadvisor.com's various Japan forums. (Just don't duplicate questions in this thread and that other forum, as that would violate FT rules.) As much as I value the FT community, sometimes I find the TA advice on specific destinations (as opposed to airlines and hotel chains) equally or more useful.
4. Not far from Kyoto, the old and somewhat less touristed historic Japanese city of Nara is well worth a visit. It's about an easy hour train ride away from Kyoto. We were fortunate enough to have an old friend show us around, but it seemed that finding your way on your own would be easy enough. Among the many highlights is an incredibly impressive, huge wooden temple and small deer that are so accustomed to people that they'll come pretty close without hesitation (though don't hold food near them or they'll reach for it!).
5. I would think that five nights each in Tokyo and Kyoto would be good. Assuming you are a Cubs fan and depending on when you are in Japan, you might want to look into attending a Japanese baseball game. It's supposed to be a real cultural experience. I'm sure the PH concierge can help if you can't arrange it on your own. I'd imagine the tickets might be expensive.
6. Actually, speaking of which, prepare for some sticker shock on many items in Japan. We found some excellent reasonably priced noodle shops that were great and some reasonably prices scarves and sweaters at little shops/stalls along the Philosopher's Path. But just accept that visiting this incredible country comes with a co$t. (If you have sufficient status at any of the hotel chains you'll be staying at, you'll save a lot via the complimentary breakfasts. If you can in fact get the Hyatt Diamond status I mentioned in a previous post, that entitles you to something like $75 per head (???) breakfast, for instance.)
7. Also be prepared that just about any hotel will be a letdown after the Park Hyatt. As I indicated, the Westin Kyoto is fine; but it's not nearly in the same league as the PH.
8. If you have Platinum status with Starwood, you'll get complimentary lounge breakfasts as well as late afternoon drinks and snacks at the Kyoto Westin. The main restaurant breakfast downstairs has a much larger spread, however.
9. The one bad piece of advice we got from the otherwise excellent concierge at the Park Hyatt was to say that just a very few days in Kyoto is sufficient. I'd say that your five nights there is a good plan, especially if you do a day trip or two.
10. I don't know enough about Osaka to know whether it's worth a night or two, as we did not make it there at all. If your flight out of there is late enough in the day and the advice you get elsewhere weighs against Osaka, you could even skip spending a night in the city entirely by simply seeing if taking a train from Kyoto and getting to the Osaka airport the same day is feasible.
11. Not sure where I'd recommend going instead if you do cut out Osaka. We spent three nights (IIRC) in Hiroshima and there is a decent and points-inexpensive Sheraton right near the train station. Visiting the city was pretty powerful, though for some reason I just was not that crazy about the museum. We also took a short trip on a (commuter-style) train and then a quick ferry from there a nearby island that I'm sorry I can't recall the name of.
12. In suggesting flying out of Osaka, I had in mind a non-stop flight from there to the USA. But your Osaka-Tokyo-LA itinerary sounds fine to me; it will save you the expense and most of the time and hassle that we had in taking the train from Kyoto to Tokyo and then on Narita.

1. We are going in mid-June. Bummer that it is the rainy season but my wife is a school teacher, so we don't have much of an option.
2. I am Hyatt Platinum (but will be tryin for a Diamond Trial before the trip), HHonors Gold, Fairmont Premier, IHG Platinum, and Starwood Gold.
3. Will DEFINITELY checkout this forum and TA forum, thanks.
4. I have made notes to checkout Nara for sure!
5. I would LOVE to see a baseball game but I need to sell my wife on it a bit. I am a large guy (6'4" - 300LBS) and am a LITTLE concerened about if I woould fit in the seat - pictured a retired offensive lineman :)
6. No problem on the co$t. We feel that we are able to take such advantage with thee hotels and flights that if we spend a few bucks while we are there that it's just part of it....not that we aren't aware of cost AT ALL, just not stressed about a few bucks here or there.
7. I am comfortable in any hotel, so even if the other hotels pale in comparison to thee Park Hyatt, I will sstill be happy.
8. I don't have Platinum with Starwood and am not sure howw to gain it since I don't get many paid nights each year. Any way to match to Starwood Platinum or gain it in another way that you know of?
9. Great, Kyoto for 5 nights sounds wonderful. If we get bored of it for some reason we can just take a few day trips.
10. I will continue researching Osaka as a destination. One thing I thought iss that it might give us a chance to get to some of the western cities that might be too far for a day trip from Kyoto.
11. I love the idea of visiting Hiroshima and was thinking of maybe a day trip from Osaka or Kyoto (I have not researched the distances yet)
12. I did not see any non-stop flights from Osaka to the U.S. mainland but I would rather get my luggage on a plane in Osaka, hang out at lounges, etc. than take a train back towards Tokyo

Thanks again!

FWIW, I've twice snagged two F seats at once on NH TPAC, most recently about two weeks ago for ORD-NRT in mid-August. 240k miles and $1,100 in YQ and taxes.

Someone already mentioned flying in to HND as an option and I'd second that as NRT is far away from the city and HND much closer if you want to save time and hassle. Plus, JAL is swapping a 787 into a 77W on the SFO-HND route both ways so there's tons of award space in F and can use AA miles.

Just booked HND-SFO on the way home on JAL in F and am going to spend a couple days in San Fran. Thanks for the idea!