If I were you, I'd just take the Keikyu train from Haneda Airport to Shinagawa in the morning and pick up your pass at Shinagawa station (any time from 09.00am). Then jump on a Shinkansen from Shinagawa to Kyoto. That way, you start earlier, with no faffing around on shuttle buses, no faffing around with left luggage, and no more cost than doing it at the airport. (the trains into Tokyo aren't JR lines - so you'll have to pay that fare anyway)

SUICA won't work on most transportation in Kyoto. There are other threads that describe all your options for Kyoto.

Yeah. And because the gates work in Yen, you'll find hundreds - or even thousands - deducted from your account. Scary stuff!
(No. In reality, if the reader is confused by multiple NFC chips in the vicinity, it will just refuse to let you through and you'll need to pull out the right card and place it on the reader).

GoogleMaps show the scale in the bottom left corner. You can get exact distances that way. Basically, most urban spaces are on a smaller scale than you're likely used to. However, in some neighborhoods (e.g. skyscraper districts in Tokyo / reclaimed islands in Kobe etc.) the scale can get pretty "inhuman".
You're welcome in retrospect.

Agree with jib-san. In the morning, just check out of the hotel, take a cab or local transportation to Shinagawa Station and trade your exchange order for the Rail Pass at the JR office there. At the same time, they will make your seat reservation for the next shinkansen to Kyoto.

Don't forget about the occasional cab when time is important. They are safe, reliable and not too expensive if you limit their use to times you really need to get someplace quickly with no hassle.

In Kyoto, you can purchase a prepaid bus/subway combination pass at the bus office just outside the Karasuma entrance of Kyoto Station, just to the right of the bus queues. They come in 1,000 and 3,000 yen denominations. The 1k yen version has 1k yen value. The 3k yen version actually gives you a bit of a discount, 3,300 yen worth of rides for 3,000 yen. Just slide the card into the slot to enter a subway platform and as you exit. Most buses have a slot at the front, near the driver where you slide the card as you exit. From Kyoto Station, you will find that routes 100 and 101 are most convenient for tourist spots.

Before you exit Kyoto Station, I recommend a visit to the Tourist Information Center on the 9th floor. Just take the escalator up to the top, turn left and follow the signs. They speak English, have maps and other information and public access computers (100 yen/15 minutes) for emailing home and such.

Apparently the hotel is 3 minutes walk from Anamori Inari station. From there the Keikyu train to Shinagawa should take about 20 minutes. Easy peasy.

LOL, I wasn't implying it would read my credit cards at the train terminals. Guess it was better to say, what is the best way to store a second card so that it doesn't cause that confusion or possible double deduction for fares?

Don't know how I missed that, but the directions to and from started working, so I have an idea of how long the walk should be. Would suck to walk 15 minutes in the wrong direction with a suit case...

Great, just what I was looking for, thanks.

All this transportation stuff is confusing, but locally we only have one bus company and one train company to get around (and of course I just get in my car). I'll have to be revising my transportation budget, since there is still so much not included with the JR Pass.

Why do you need a second card?

I used to carry one card in my wallet for business use and then use my mobile phone for personal travel. Then I would print a record of trips I made using the "business card" in my wallet and make an expense claim. Since I no longer have a Japanese mobile phone, I just use one card, print the journeys and cross out the personal trips.

It's not a good idea to keep two SUICA cards in the same purse. You won't be double-charged, but the barrier will shut and you'll hold up the human traffic trying to go through the gate.

I probably won't, but I misread the article I was reading anyway. Looks like you still have tap the card on the reader, so I just need to select the right one.. It's not like driving thru EZ-Pass like thought....

Still trying to hash out an itinerary. I will be there for 12 nights and 11 days, odd... lol.

Night 1 Hotel Jal City Haneda Tokyo (Nothing else much I can do since the flight comes in at 10:30 PM)

Do JR Pass exchange and head to Kyoto in the morning.

Night 2-5 Karasuma Kyoto Hotel

Night 6-7 No hotel booked, try a ryokan, hostel, or capsule hotel?

Night 8-11 Sakura Hotel Ikebukuro

Night 12 Hang out at airport/sky lounge? (Flight at 6:55 AM)
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*Plans in Kyoto area*
Fushimi Inari Shrine - Looks neat
Kinkakuji (Golden Pavilion)
Kiyomizudera Temple - looks like a good view
Himeji Castle -May skip, it's under renovation
Monkey Park Iwatayama- Yes, feed the monkeys... May skip, seems a little out of the way so far.
Gion - Will likely be to late for the festival, but may spot some Geishas

Osaka Aquarium?
Osaka Castle (Osakajo)?

Hiroshima/Miyajima

*Plans in Tokyo area*
Sunshine City - hotel right in that area.
Sunshine International Aquarium - under renovation, but should be open by the time I am there. (a visit to Tokyo Sea Life Park might be sufficient for my aquarium needs though)

Akihabara for browsing, probably can get better deals on stuff at home.
Ginza
Tokyo Metropolitan Government Building

Disney Sea - Probably half a day and get the 1/2 price evening ticket

Thinking about getting the Grutt Pass for 2000 yen
http://www.rekibun.or.jp/grutto/museum2011.html
Includes 3 Zoos including Uneo Zoo
Plus Tokyo Sea Life Park
and National Science Museum of Japan where I think Hachiko is..
Then there are a bunch of other museums I might visit if they are close by.

The Ramen Museum - get a free ticket from my hotel...
Yokohama Chinatown -

Mount Fuji - maybe?

==========================
The 2 nights without a hotel were originally saved for Hiroshima/Miyajima, but looks like I might not need that much time in Kyoto and might just head back to Tokyo early.

Still more stuff I could add I am sure...

Deleted, I answered a post that was long ago but at the bottom of the first page (which fooled an innocent like me).

Thanks for the effort though

You can't run out of things to see in Kyoto in just a few days.

Some additional ideas: Nijo Castle, Sanjusangendo Hall, Heian Jingu Shrine, Ryoanji Temple. Instead of Himeji Castle, use your JR Pass and take the local train to Hikone on the shore of Lake Biwa to see Hikone Castle. Day trip to Nara.

Thanks for the additional ideas. There are definitely lots of castles/temples/shrines to visit, I'm just not sure if I will be interested in those. I do like animals, hope I get to see some shiba inus , maybe I'll visit one of their doggy cafes.

Perhaps you'd enjoy meeting the deer in Nara.

I was going to skip those, because there are suppose to be deer in Miyajima. Though looks like Nara has lots more deer and I'm a sucker for feeding the animals.

Todaiji temple looks impressive too^

I started plotting places on Google maps, so I can see what is close together to plan my time accordingly.

Any recommendations of Android apps (preferably not needing data) that might be useful? Got the hyperdia lite app and some Japanese phrase apps.

Getting things finalized for my trip
One more quick question, when making a reservation for the Shinkansen, is there like a seat map you get presented with? I wanted to get a seat near the end so I can put my luggage behind the seat..

No map. Just tell the agent. It can be a problem, though since the seats swivel around to face the other direction at each end of the run. Kind of hard to know if you want a low number or a high number. Feel free to just dump your large bags in that space and continue on to find your seat number. Nobody will mess with them. Small bags, like my little backpack/camera case can go overhead in the rack above your seat.

Just though I would update with some thoughts and experiences after my trip:

OMG those Shinkansen trains are long. I got a seat reservation for my first trip and could not make it to back of the (like Car 13) train in time. The train was already there when I made my way onto the platform, in retrospect, I should of just jumped on any of the cars and just made my way back to the car or even just got on the unreserved seat cars. The cars are "sealed" between each other, so it's not like you would fall out, which I have always feared when moving between cars...

You don't always need a seat reservation either, I nearly forgot this when I was trying to get a seat reservation and the guy told me sold out. Actually I asked if I would be able to get an unreserved seat and he still said sold out. I found out which platform the Shinkansen was going to be on and just waited in the unreserved seat car line, and got a seat . Otherwise I was looking at a ~2 hour wait for the next train as it was rather late.

For the most part, I never really had a problem getting on the trains that worked for the JR Pass. Only once did I have trouble finding the manned gate (basically they had lots of gates at one of the stations in Tokyo, but only one was manned).

Once, I was in Tokyo (and JR pass expired), I just got the daily JR pass for 730 yen each day. There were days when this paid off and days where I probably should of just bought individual tickets. However, it all balanced out in the end. I did not have to bother with buying and returning one of the Suica cards..

Kyoto definitely made a good base. I made a day trip to Osaka and did not really like it. It just did not feel as tourist friendly (I did not seem to find maps or any guidance to attractions when coming out of the subway stations).

Only other thing I would have liked to have done is figuring out the exits better as the subway/train stations have lots of different exits. Google maps made it look like I would have to walk 3 blocks, but there was literally an exit that was practically in front of my destination.

The public Sky lounge at Haneda is after security (there were some TIAT waiting lounges like right next to the Delta desk that I mistook for the Sky lounge). I was able to check in my luggage the previous evening at around 11-12 for my morning flight at ~6-7. They were checking in the Los Angeles at the time, so the agent went to check with someone if they could check me in.

Sky lounge was 1000 yen for entrance, showers are another 1000 yen for up to 30 minutes. Still cheaper than a night at a hotel and I was able to nap for a few hours in their little cubes with comfy chairs. There were soft drinks at no charge, but alcohol and snacks were also available for a fee.