Classical Japanese poetry is conventionally transcribed (and read) as if it were written in modern Japanese – that, at least, is the way you will find it in most published anthologies. This has the unfortunate effect, though, of suggesting that the Japanese language has remained unchanged throughout the past 1400 years, and gives no impression of what the poems sounded like to their composers and original audience.
The poems here, then, will be transcribed in a way which reflects the linguistic context of their composition, whether that be Early Old Japanese, Late Old Japanese, Middle Japanese or Early Modern Japanese. Hopefully, this will allow you to savour the sounds of the poems as well as their sense! Check out Nic Tranter’s article on Early Old Japanese phonology to find out more detailed information on the language of the Kojiki and Man’yoshu.