Well, this appears logically doable,
but I recommend you check the cancelation policy of your Kyoto accommodation
and, if you can, make it start from the following day instead.
You will visit the Kawaguchiko area on a Saturday,
probably during the peak of the autumn color foliage,
so it should be better to expect crowdedness.
9:05am arr.11:40am OR 10:20am arr.12:55pm Airport Limousine Bus The departure time you cite is for the bus stop in HND Domestic Terminal 1.
The buses depart earlier by 15 minutes from HND International Terminal.
http://hnd-bus.com/airport/h-kawaguchiko/ Haneda Airport International Terminal
{08:50} / {10:05} Airport Limousine Bus
{11:40} / {12:55}
Kawaguchiko Railway Station.
5pm arr. 6:38pm OR 6:30pm arr. 8:08pm Highway Bus Kawaguchiko to Mishima To travel with Japan Rail Pass from Mishima,
you had better catch the former bus at Kawaguchiko.
Taking the latter bus, you may miss the 20:24 Shinkansen train.
The last Shinkansen connection
for Japan Rail Pass travelers:
Mishima
{20:24} [KODAMA 683]
either
{20:51} Shizuoka
{21:10} [HIKARI 533]
or
{21:21} Hamamatsu
{21:36} [HIKARI 533]
{23:01}
Kyoto.
The last Shinkansen connection
for regular ticket travelers:
Mishima
{20:57} [KODAMA 685]
{22:45} Nagoya
{22:48} [NOZOMI 263]
{23:21}
Kyoto.
How is the rest of your itinerary?
I wonder how a Japan Rail Pass can pay off,
because you will go by JR only beyond Mishima
on your way from Tokyo to Kyoto.