Hi Tracey!
Sorry to bring you some bad news but access to Fujikyu involves a lot of travel time. From Tokyo this is mainly done by express bus taking 2-3 hours, either from Tokyo or Shinjuku stations.
The hard part is going from Fujikyu - Kyoto which takes over 5 hours of travel, the route being Fujikyu - Gotemba by bus (about 2H) then the train Gotemba - Kyoto which is a little over 2H, add in transfer time and travel time to your accommodation and it may be well over 5hours, leaving little room for sightseeing.
A better option would be to stay the night around FujiQ or Kawaguchiko and travel on the following morning, additionally there is a night bus service from FujiQ to Kyoto/Osaka.
Hope this helps!
Daniel