I second the idea of staying at the Regal by the airport, then taking the best part of the next day to explore Lantau Island...go to the giant buddha statue and park. Enjoy a side of Hong Kong most visitors don't get to experience because they head into Kowloon or onto Hong Kong Island. (I believe the Airport Express is free to this and the shopping centre stop.) Unless there is another reason for heading into the "colony" proper, make the stopover a restful experience -- and you'll probably save money and the hassle of all these transfers.

But if you do opt for the Grand Stamford, the Airport Express is the best and most economical way to do it. Get a return ticket from the kiosk, stop by an ATM for a few HK$s to pay for incidentals and a cab, and then hop the train into the Kowloon station. From there, the shuttle buses will get her to the hotel, or grab a cab. On the return, she should head for the train around noon. She can check in at the Kowloon Airport Express station and take the ride back to HKG terminal. (By cab or shuttle, give her an hour to get from the hotel to the AE station, only because of the heaviness of traffic in this part of the city at this time of day.)

(Of course, there is the underground walk to the MRT station from the Stamford, then a ride across to Central Station and get on the Airport Express. I would not recommend this convoluted way of doing it, any more than the STAR Ferry idea.