Advice on Itiniery

I'm planning my first vacation in Japan, I posted before for some advice & have redone my Itiniery and would like some advice whether it is feasable or not, as well as any advice on some other places to go.

What I'm planning is
Day 1 - Enter KIX
Day 2 - Kyoto
kyomizu-dera
ninen zaka & sannen zaka
shoren-in chion-in sanjusengen-do gion
Day 3 - Kyoto
nishiki market
manga museum
kyoto tower
nishi hongan-ji
shosei-en
Day 4 - Kyoto
kyoto imperial palace park
to-ji
kyoto botanical gardens kamigamo-jinja
Day 5 - Kyoto
fushimi-inari taisha nijo-jo
Day 6 - Osaka
osaka-jo nakano-shima dotombori
doguya suji arcade amerika-mura
umeda sky building
Day 7 - Himeji
himeji-jo
koko-en
engyoji
Day 8 - Nara
nara koen area kofuku-ji todai-ji
isui-en
imanishi seibei shoten
Day 9 - Travel / free day
Day 10 - Nikko
shin-kyo rinno-ji tosho-gu
tamozawa goyotei gamman-ga-fuchi abyss
kegon-no taki
akechi-daira ropeway
Day 11 - Tokyo
senso-ji
tokyo national museum ueno-koen
ameyoko arcade
Day 12 - Tokyo
tsukiji fish market imperial palace grounds imperial palace east garden
kitanomaru-ken hie-jinja
tokyo tower
Day 13 - Tokyo
yoyogi-koen
sunshine city
Day 14 - Tokyo
yebisu garden palace
fuji tv
Flame of liberty
Day 15 - Tokyo
Free Day
Day 16 - Tokyo
Free day
Day 17 - Leave Narita

I'll be making Kyoto & Tokyo my bases. So for the first half of the trip I'll be heading back to Kyoto every day after the day trips.
I would like to stay at a ryokan onsen at one night along the trip, not sure where but if anyone has any reccomendations it would be appreciated.

The day in Nikko seems a little bit busy. Especially if you like a slower travel pace, it might be better to stay overnight in Nikko and spend two days there. If you like a fast pace, though, it can be done.

I thought it might be a bit much, I was thinking of either staying at the ryokan at Chuzenjiko or dropping the last 2 from the day in Nikko, both of which are at Chuzenjiko. Still though it might be a bit much then even.
I'll have to re-evaluate what sights I want to see there.
Does anyone know the approximate travel time to Nikko from Tokyo, not sure what area I'll be staying in so any rough idea will help.

Also I was thinking of getting & using a 7 day Rail pass for the mid section of the trip where im doing travel. Does anyone reccomend this, or will it be better to get a different pass?

Also is there a Tokyo subway pass that anyone knows of? I mean unlimited travel on the loop, or something like that for when im doing Tokyo.

Does anyone know the approximate travel time to Nikko from Tokyo, not sure what area I'll be staying in so any rough idea will help.

Here you go:
http://www.japan-guide.com/e/e3805.html

Also I was thinking of getting & using a 7 day Rail pass for the mid section of the trip where im doing travel. Does anyone reccomend this, or will it be better to get a different pass?

No, a 7-day Japan Rail Pass does not pay off for your itinerary. But a 1-day JR West Kansai Pass is cheaper than regular tickets for the side trip to Himeji.

Also is there a Tokyo subway pass that anyone knows of? I mean unlimited travel on the loop, or something like that for when im doing Tokyo.

Day passes are explained on the following page, but I recommend to use a prepaid card (Suica) rather than day passes, because the day passes are inconvenient (most do not cover everything) and rarely pay off:
http://www.japan-guide.com/e/e2017.html