So repetition only applies to one side not overall board position?
No, the whole position has to be repeated three times, with the same side on the move each time. If castling was possible in one of the positions, it has to be possible in all, and if en passant was possible in one of the positions, that one won't count for repetition since it wouldn't be available in the latter ones.
Black to move after:
43.Rd4
45.Rd4 and
47.Kf2
is the same position.