The conjunction fa- links the next action. Yabtadiʾu is an imperfect verb, Form VIII, from the root b-d-ʾ, meaning 'to begin.' Its implied subject is he, the pilgrim.
Bi-jamrati is a prepositional phrase; al-ʿaqabati is the genitive complement of the idafah. The sentence identifies the starting site, not the count of pebbles.