Hello,
Are you going to Kyoto directly from Mt. Fuji? If so, you can take a night bus operated by Fujikyuko Bus. It departs Mt. Fuji Station at 20:45 and arrives at Kyoto Station at 5:57. The website below says it costs 6,900 JPY, but a Japanese booking website says 8,200 JPY. There are no cheaper seats left on September 6 according to the Japanese booking site. Please call 0555-73-8181 for your reservation. I think that English service should be available on this number.
http://bus-en.fujikyu.co.jp/highway/detail/id/9/
You can also take a JR Shinkansen Kodama from Shin-Fuji Station to Kyoto. The last train leaves Shin-Fuji Station at 20:39 and arrives at Kyoto Station at 23:11. It cost 10,890 JPY including seat reservation fee.
Please note that you have to take a local bus from Mt. Fuji 5th to Mt. Fuji Station or Shin-Fuji Station.
I hope you have had a great time in Japan!