Is it permissible for a man to throw the pebbles (at the Jamarat) with stones collected by his wife, and what is the ruling on a husband throwing on behalf of someone else with pebbles he believes his wife collected some of, and is it valid to throw on behalf of someone performing Hajj on behalf of his father without the thrower being aware of that?

There is no harm for a pilgrim to throw with pebbles that someone else picked up for him, and there is no difference in this between a wife or someone else. The supervisor did well when he returned to Mina and threw after zawal (midday) to rectify his error in appointing you to throw on his behalf without necessity, and his departure from Mina before you threw on his behalf, and his throwing before zawal.