Japan's major city I'd guess would either be round about where modern Kyoto/Osaka is, or in old Yamato province (nara prefecture) depending on how the alternate history panned out. having the main centre be in Kyushu or in the north would be unrealistic for various reasons)
Pretty good guess.
Its actual capital is a tad south of Nara proper, in what's now the city of Tenri.
For further information, and for information I apparently didn't put in my big city post (whoops), the capital's name is for now:
The Grand Capital of the Divine, Blessed by Heaven, Temple of the Immortals, Sanctuary of Amaterasu, Infinite Seat of the Great King, Extension of His Solar Throne, City of the Ten Thousand Shrines, Impregnable Fortress of the Gods Beloved, Home of the Palatial Lanterns that Offer Sacred Light upon the Ephemerality of That the Swift River
[神の大京 天恵 仙の寺 天照大御神の聖域 治天下大王の無限な座席 治天下大王の太陽座の波及 万神社市 神愛無敵な要塞 あの迅速な川へ神聖な光を授ける豪華な灯籠の家
Kami no Daikyō Tenkei Sen-no-tera Amaterasu Ōmikami-no-seiiki chitenka daiō no mugen'na zaseki chitenka daiō no taiyō-za no hakyū Jinja-shi shin ai muteki man na yōsai ano jinsokuna kawa e shinseina hikari o sazukeru gōkana tōrō no ie]
Or for short, Kami-no-Daikyō, Daikyō, or Miyako.