It has to do with Little Yus (Ѧ) as well as the Big Yus (Ѫ), which morphed into ya and ye. There was also some confusion as to how the perosnal pronoun (which used toba Az but then became Ya), and how it was spelled. I already mentioned Radoye in a 12th century Bosnian document where he uses "Ѣ" instaed of "Я" for a personal pronoun.
By the way, I have read someowhere that in early 1700 hundreds, the "ѣ" had a distinct vocalization in Russian, but by the time of the great orthographic reform in the latter half of the 18th century, Lomonosov wrote that there was no audible difference between the "ѣ" and and an ordinary "e". However, for some reason the yat was retained until 1917. Other sources indicate that in some regions the "ѣ" is still audibly distinct from the Russian "e".
Thank you -- I did not know any of that.
Although Church Slavonic sounds and looks "Russian," it is grammatically much closer to Serbian.
It is true that Serbian and to a lesser extent Bulgarian are closer to the Church Slavonic than Russian. Till I learned Bulgarian I could not understand the Church Slavonic.