How is your full itinerary? Do you plan to use a Japan Rail Pass?
it take about 90 minutes. Yes, if you start from near Kyoto Station and use Tokaido Shinkansen from Kyoto to Nagoya, it usually takes about 1 and a half hour. It might take 2 hours depending on connections (of a few trains and one bus) and also on the road traffic of the bus line.
During the last illumination season of Nabana no Sato (from 25 October 2013 to 31 March 2014), direct Mie Kotsu Buses [Sanco Buses] connected Kintetsu-nagashima Station and Nabana no Sato. Buses to connect Kuwana Station(s) and Nabana no Sato were not available during the season.
Now it is not clear whether such seasonal buses will be available on the same line during the next illumination season of Nabana no Sato from around the end of October 2014. (I guess they will.) If Mie Kotsu plans to operate the seasonal buses again, I suppose the timetables will become available by September 2014 and its buses from/to Kuwana Station(s) will again not be available during the season.
The following day we catch a train back to Tokyo and must be back in Kichjoji at a reasonable time. Any recommendations on the quickest route? Well, it takes about 3 hours to 3 and a half hours to travel by rail from Kintetsu-nagashima Station, Kuwana Station of Kintetsu or Kuwana Station of JR to Kichijoji (not Kichjoji) Station of JR.
One of the quickest routes by rail is
Kintetsu-nagashima
| [Kintetsu: Train for several minutes (#1)]
Kuwana (#1)
| [JR: Rapid "Mie" train for about 20 minutes]
Nagoya: Shinkansen North or South Transfer Gate (#1)
http://english.jr-central.co.jp/info/station/_img/nagoya_L.jpg| [JR Tokaido Shinkansen: "Hikari" or "Nozomi" train (#2) for about1 and a half hour]
Shinagawa: Shinkansen transfer gate then Track 2
| [JR Yamanote Linefs outer loop: Train for about 20 minutes]
Track 15: Shinjuku: Track 16 (beside the same platform)
| [JR Chuo (Sobu) Line: Local train for about 15 minutes]
Kichijoji.
(#1) Kintetsu platforms of Kuwana Station have staircases and seem not equipped with escalator or elevator. You can avoid using a staircase if you alternatively take a Kintetsu train (for about 30 minutes) through to Kintetsu-nagoya Station and make a transfer (for about 10 minutes) to JR Tokaido Shinkansen via Shinkansen North or South Ticket Gate of Nagoya Station.
(#2) Here Nozomi is slightly faster than Hikari. When you travel with a Japan Rail Pass, you cannot choose Nozomi.