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.