1)
When did they separate the Arei Miklat in Ever ha'Yarden?
1.
Rashi: It was in the days of Moshe (Devarim 4:43).
2)
Why were there three Arei Miklat for two and a half Shevatim in Ever ha'Yarden, and three for nine and a half Shevatim in Eretz Yisrael proper?
1.
Refer to Bamidbar 35:14:1:1-3 and the notes there.