POSSIBLE SPOILERS BELOW!
Ok rewatching it and step by step I've worked out a lot, not all, of how he did it. I'm no card wizard so this is just amateur deduction from observation.
2.39 - the deck has been cut three times - the way he's cutting the deck does NOT re-order the whole deck as he suggests, it just pushes it along so the order is the same just the beginning and end are in differnet places.
2.41 - He then opens the deck and looks at a card - I THINK he is then judging where in the deck it's cycled through to and is correcting it. It could also be he's found his marked card
2.50 - It APPEARS that perhaps this three way cut he does here does nothing but puts the cards back in the same order.
2.59 - BIG ONE HERE which is VERY easy to see - when he cuts the card, he grabs half the deck and just spins it, making it look like he's cut the card but hasn't. I expect many of his other cuts are similar tricks made to look like he's reordering the cards when he is in fact not.
3.03 - same as above, shown from a different angle.
3.09 - slightly different, cuts the cards, looks at them, and replaces them back to how they were.
3.18 - yep, got the number of the guy now. Look at this shuffle. Look at it again. And again! Notice he's splitting the deck into three chunks, then placing them back again in the same places without actually reordering them.
3.22 - spin shuffle again. I'll stop mentioning these now as he does them a lot!
3.43 - I'm stumped! The girl cuts the cards, he doesn't appear to manipulate them but somehow pulls the desired card from the top. Damn you magician!
EDIT Only thing I can think is at 3.43 after he picks up the deck he switches it. The deck is pretty small now so this would be a lot easier to do than with a full deck, which would also explain the sudden appearance of the 'what the hell' card.
So in summary, once the three volunteers don't shuffle but just move the order of the cards along he then looks for a marked card to put his starting card back to the top. After this he does various fairly cheap movements to make it look like he's constantly shuffling the cards but he isn't. When it gets close to the end, he gets the girl to cut the cards a final time which is a ruse to disguise the replacement of the deck.
