Ok, this might turn into a long post, just warning you.
First, you have two weeks. So,
forget Tokyo. The place is huge, overwhelming, way too crowded, and horridly expensive.
Well, you don't have to
forget Tokyo, but you have two full bloody weeks. So I
strongly recommend not spending more than 2-3 days in Tokyo. (The only reason I kind of enjoyed it was because my uncle had a house in Shibuya--yeah, a house--while I was there, so I had free lodging and meals. Even then I tried to get out to the surrounding prefectures).
Step 1: Getting Around
Now then, because you have two weeks, I highly recommend getting a JTB JR pass. There are several different rail companies in the country, but JR is nationwide. You can purchase a pass from the Japan Travel Bureau (
http://www.jtbusa.com/). Check the JTB Pass page here (
http://www.jtbusa.com/enhome/jrpasstop.asp)--I recommend either getting the JR Pass which covers all lines, or the JR West pass since that's where Kyoto, Nara, Hiroshima, Miyajima, and Osaka are.
Now, the JR pass is an unlimited-use pass for most JR lines, but
not the Shinkansen lines--Shinkansen is a bit expensive ($100 to get from Tokyo to Nagoya, more to go further like up to Kyoto, Hiroshima, or Osaka). The down-side is that the JR trains you can get on will be slower (it's 2 hours by Shinkansen to Nagoya, but 4 hours by regular JR lines). It depends on if time or money is your greater concern--but still, don't stick around in Tokyo! You'll miss the better parts of the country!
Anyway, when planning a trip to another city, then you should either be pretty good at reading rail maps, or you should ask someone at a tourist center. If you're ever unsure about if you can board at a platform with your JR pass, then just show the pass to the attendant at the gate and ask (in English, preferably) if you can go on the train with that. 99.9% of the station attendants will be extremely helpful, even if they can't entirely understand you.
Step 2: Lodging
Lodging is typically very expensive, and depends on how comfortable you are with different kinds. 3/4-star hotels, particularly in cities, can range from expensive (in major cities) to unaffordable (in Tokyo--which is why I'm saying not to spend too long there). You might find some good deals, though, depending on how you booked.
As for alternatives to hotels, there are two. The first is hostels. You'll typically have to look these up online or elsewise before going, be pretty good with directions, and be comfortable with sharing rooms with strangers. Keep in mind that, even though you're going with your husband, many will not allow men and women to sleep in the same room. Also, some might not have showers or baths in the building itself, but you'll need to go to a public bathhouse for that--now, I happen to like them, but they're not for everybody.
The second are ryokan, or Japanese-style inns. These can be quite expensive, and I don't recommend them generally, but
please try to stay in one for at least one or two nights! They're incredibly comfortable, and the staff can be incredibly hospitable. You won't regret it. (I'll recommend below where I think you might should stay in one.)
Step 3: Eating
Every place has a specialty. In Hiroshima it's okonomiyaki, in Nagoya it's kishimen, in Tochigi prefecture it's soba. If you can find out the local specialty, try to find a restaurant that specializes in that, well, specialty (in Hiroshima it's easy--look for a stand with barstools around and a guy making okonomiyaki in the middle).
If you're staying at a ryokan, then try the meals there at least once (the decent ones will have a dining room or something similar where you can be served). Once is enough 'cause you'll eat like royalty. Hey, it's your honeymoon, you should go all-out... at least somewhat.
On the road, most shops will specialize in a certain type of food or cuisine. You can usually tell on the outside what they have, and even if no one there speaks English, they'll understand if you point at a particular item (and prices are listed with tax included, always, and there's no tipping--so what you see is what you pay). But, general rule of thumb is that if it looks good, then go ahead and try it. Except natto, but that looks disgusting anyway.
Kaiten-zushi (conveyor-belt sushi) is another good stop, particularly if you're not very hungry and don't want to pay a lot. Pay attention to the pricing scheme they have (most price it by the color of the plate, ranging from 100Yen to 1000Yen); they'll typically also have 'sides' like shrimp miso soup if you ask for it ("ebi miso shiru"). Don't trust places that have all 100Yen plates, though.
If you want to go bar-hopping, then make sure you check out an izakaya (居酒屋) and not a 'snack' (スナック). The latter are usually in shadier places anyway. Izakaya can have a really nice set up and typically have really good food with them as well.
Step 4A: Tokyo
If you
must stick around Tokyo, then I'll give a quick rundown of some of the places I liked... These are all downtown, and you can make the circle on the Yamanote-line (the 'green line' for the JR) on all these major spots. (The stops are named after these places, too.)
Shibuya
Pretty vibrant nightlife, even if you just feel like wandering the streets. Which is usually what I did. This is usually where folks from about 16-25 or so hang out.
Roppongi
Don't go at night unless clubbing or bar-hopping is your thing (that being said, most Japanese bars--izakaya--are pretty good places). If you go here in the daytime, then go to Roppongi Hills--it's a massive shopping and cultural center for the area (
http://www.roppongihills.com/en/).
Harajuku
This is fun to go just for people-watching. You can see tons of girls going around in all elaborate Gothic Lolita costumes. Don't be afraid to ask for a photo.
Ueno
The park is lovely. If the fall colors are coming in the trees, then I recommend going to Ueno Park.
Akihabara
This was my favorite place in Tokyo. Make sure you exit out the end that says "Electronics Town" (電池町, I think--it'll look like:
http://www.youtube.com/watch?v=ljnsn2_Hs8Q). The major-name shops are Tora no Ana (books and manga--don't browse the doujinshi), LAOX (games and more), and ASO Bit City (games and more, but they were renovating or something last time I was there--but that was in 2004). I also really like going onto the side roads and checking out back-alley used game shops, but have a decent sense of direction if you want to do that.
There's also all the usual tourist spots, like the Meiji Shrine and what not. In all honesty, I found them bland. The Meiji Shrine you can't go that far into, and even if you can it's so bloody crowded. If you skip it you really won't miss a whole lot, if you ask me...
Oh, and Yokohama... There's the port and not a whole lot else except for really big buildings. If you ask me, I'd skip it altogether and use the time to get elsewhere in the country.
Step 4B: Mt. Fuji
Mt. Fuji is beautiful, and takes an entire day to check out. Make sure you have some reliable transport to get up towards the top (your friend, if he has a car, might be able to help you out there). Since it seems you're already planning on this, I'll move on.
Step 4C: Nara
Nara has a stop on JR, but not on Shinkansen if I recall correctly... It comes before Kyoto if you're headed from Tokyo's direction.
Nara takes just one day to go around most of it. While there, make sure to see the Daibutsu (the giant Buddha statue) and some of the major temples there. You can pick up a map of the area (most of it is walkable--there's little or no mass transit within the city) from any tourist center or kiosk there.
The biscuits in the street vending machine are for the deer. Don't buy them as souveniers for people unless you really don't like them.
Step 4D: Kyoto
I have a curse with Kyoto. If I go it rains. Heavily. There's a saying that Kyoto looks best in the rain, but I don't have any basis for comparison. You'll probably want to spend 2-3 days here for a comfortable vacation.
Anyway, when I went last time, I stayed at a youth hostel with some friends. You might want to spring for a ryokan instead, although since it's tourist central for Japan then those might get real expensive. So plan accordingly.
Now then, there're a million shrines in the city. Take a tourist map from a kiosk or someplace, and check out the ones you want to see. If you and your husband don't mind a lot of walking, walk around downtown to most of the places--you might just happen upon a shrine, cemetary, or other lovely landmark along the way. The main thing to see is probably the "Golden Temple", in the west side of the city.
Kyoto has a small subway system, and a bus system. I had no problem with the bus, but other people I know have had problems with it. Hence, well, walking and perhaps 1-2 taxi rides might be a better bet for you.
Step 4E: Osaka
Osaka is the second largest city in Japan. ...I've never been, so sorry, I can't help you there. It's a short distance from Kyoto, however, so it'd be your next stop if you want to stay here.
Step 4F: Hiroshima
Hiroshima is a really, really wonderful city. You can spend 1-2 days here. You'll have to see the Peace Park in the center of the city, just south of where the bomb fell. If you like baseball by chance, the Hiroshima Giants stadium is a bit northeast from the park.
Hiroshima has a convenient light rail system that goes through most of the city, and further south to a port where you can get to your next stop...
Step 4G: Miyajima
Miyajima! Go to Miyajima! Seriously, if you go to no other place in Japan, then at least go here! You can spend 2 or so days here, but hell, I could spend an entire week.
Miyajima is just off the coast of Hiroshima. It's absolutely, positively gorgeous. It's where you'll find the Ise Shrine (with the famous Torii gate), more deer like in Nara, and some wonderful natural scenery. Hike up the trail to the top of the mountain / hill there; you'll catch the most beautiful scenery in the entire country.
This is one place where, if nowhere else, you want to stay at a ryokan. The one I stayed at had a bath at the top of the inn, where I stopped in at sunrise each day (most folks take baths in the evening though).
If you're comfortable enough, you might want to try checking out an onsen (hot springs) some time, at any point along your journey. Obviously you and your husband won't be going into the same one (there are some mixed-springs, but they're rare). I
should warn you, though, that some of my female friends have had issues with women bringing their male children in--babies are typically acceptable, but some women don't get the hint when their boy is, like, 6-7 years old that he shouldn't be there.
Step 5: Other Places
So... Other places might include Nagoya, which is a great city to live in but unfortunately doesn't offer a lot for tourists. Karuizawa, which is up in the mountains near Nagano and has tons of wonderful hot-springs and baths. Sapporo in Hokkaido (way to the north). And Okinawa (wayyyyy to the south--you'll need a flight to get there).
If these places are starting to interest you, but you're worried about knowing how to get there, let me know. I might be able to help you actually plan getting between cities, since most schedules are available online.
Phew! That was long! I'll answer some other questions you brought up here sometime later. KF
I'm really excited and I'm beginning to think there might be something wrong with me since I'm not nervous ^^; Everyone keeps asking if I am though :p
I'll definitely be going to Tokyo/Shibuya, Akihabara, and possibly Yokohama and we're planning on climbing Mt Fuji while we're there as well. I'll of course keep an eye out for any Lunar sightings! 
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Did you use to live in Japan?
