Make sure to get Nara World Heritage three day pass -Nara, Ikaruga, Yoshino Areas-(Nara Sekai Isan Frea Kippu -Nara, Ikaruga, Yoshino Areas-) at Kintetsu Railway stations (below). It's valid only for Kintetsu Railway and Nara Kotsu Bus services(not for JR), but covers all the transportation expenses of the following itinerary (except Yoshino Ropeway). Tell the ticket clerk on what date you will start using it and you can get a pass one month in advance.
This three day pass costs:
2800yen(1400yen for a child), if traveling from Osaka(Namba, Nipponbashi, Uehonmachi, Tsuruhashi stations on Kintetsu Line), gaining 1690yen discount.
3000yen(1500yen for a child), if traveling from Kyoto(Kintetsu Kyoto statioin), gaining a 1630yen discount.
This itinerary is based on the WEEKDAY timetable, and may vary on Saturday, Sunday and national holidays.
Also bring this PDF MAP of railways in Nara with you.
Rapid Expresses(快速急行) depart from Namba station at 8:38, 8:51, 9:04, 9:13, 9:25, 9:37, 9:44, 9:55, 10:07, 10:17, 10:24, 10:32 and arrive at terminal Nara Station between 9:17 and 11:10, also making stops at Nipponbashi, Uehonmachi, Tsuruhashi stations in Osaka. No change is needed.
Expresses(急行) depart from Kyoto station at 8:39(for Nara), 8:52, 9:09, 9:24, 9:39, 9:52(for Nara), 10:10, 10:25 and arrive at Nara Station between 9:27 and 11:15.
On your way to Nara, stop at Yamato-Saidaiji Station and walk to the Heijo Palace Site(WH) (appr. 15 minutes). The grounds are quite vast, so if you choose to visit the museums (at opposite ends of the area), you may be pressed for time to see the rest of the day's sites, depending on how long you take to see each. It may be wise to give the museums a miss, as they are not of any great interest. At the very least, walk to the center of the grounds to see the actual excavation site and the remnants of the old imperial palace. You may also enjoy seeing the Suzakumon Gate, although it is a modern reconstruction.
Go back to Yamato-Saidaiji Station and head to Nara Staton where you will find the rest of the days sites.
You can best manage your time by visiting the sites in the following order (You will go through the Kofukuji area on the way to/from Gango-ji Temple, so order is not as important here.) The others are listed in the order you will pass them walking away from the station:
Kofuku-ji Temple(WH) (admission free in the premises, open 24h)
Gango-ji Temple(WH) (admission 400yen, open 9:00-17:00)
Todai-ji Temple(WH) (admission free in the premises, 500yen for the Main Hall, open 8:00-16:00 in Nov to Feb, longer in the other months)
Kasuga Taisha Shrine(WH) (admission free in the premises, open 24h)
Kasugayama Premeval Forest(WH)
Note that the three day pass is valid for Nara Kotsu Bus service in central Nara.
In the morning, catch the train from Kintetsu Nara station to Yamato-Saidaiji station(2 stops from Nara) and then to Yoshino. There are lots of commuter service between Nara and Yamato-Saidaiji stations, arriving at Yamato-Saidaiji every 10 minutes.
Expresses(急行) depart from Yamato-Saidaiji station at 8:22, 8:41, 9:28, 9:52, 10:23 bound for terminal Kashihara Jingu Mae station(7 stops). Change your train there for terminal Yoshino Station.
Mt. Omine and Onsen
It's extremely difficult to get to Ominesan-ji Temple(WH) in Mt.Omine(WH) by public transportation, but you can find authentic ryokans in Dorokawa Onsen Village in front of Mt.Omine if interested. Women are not permitted to climb this mountain, as a part of religious tradition.
Expresses(急行) depart from Kashihara Jingu Mae station at X:07 and X:37 every hour between 11 and 15, 16:08, 16:37, 17:08, 17:39, 18:08, 18:38, 19:08, 19:40, 20:06, 20:35 and arrive at Yamato-Saidaiji station(7 stops) in 30 minutes. There are lots of commuter service between Nara and Yamato-Saidaiji stations, arriving at Nara in 10 minutes.
In the morning, catch the bus on Nara-Nishinokyo-Ikaruga Excursion Bus line(Line No. 97) from Kintetsu Nara(at 8:43) or JR Nara(at 8:45) stations to terminal Horyu-ji(E-15)(at 9:43) and Hokki-ji(E-13).
In the afternoon, catch the bus(Line No. 97) at 12:43 or 13:43 to Yakushi-ji(E-10) and Toshodai-ji(E-8). The distance from Yakushi-ji to Toshodai-ji is 600m and can be covered on foot. The latest bus departs from Toshodai-ji(E-8) at 16:23 and arrives at Kintetsu Nara station at 16:40.
Horyu-ji Temple(WH) (admission 1000yen, open 8:00-16:30 in Nov to Feb, 30 minutes longer in the other months)
Hokki-ji Temple(WH) (admission 400yen, open 8:00-16:30 in Nov to Feb, 30 minutes longer in the other months)
Yakushi-ji Temple(WH) (admission 800yen, open 8:30-17:00, the latest entry 16:30)
Toshodai-ji Temple(WH) (admission 600yen, open 8:30-17:00, the latest entry 16:30)
Expresses(急行) depart from Kintetsu Nara station directly bound for terminal Kyoto station at 17:17, 18:16, 19:16, 19:49 and 20:17. The journey takes less than an hour, arriving between 18:03 and 21:03. If you miss these trains, catch the train for Osaka(above) and change the train at Yamato-Saidaiji station(2 stops from Nara).