But when Waterhouse, who had just received medical sign-off for her transition, listed her recent doctors' visits --- "wisdom teeth out, gender transition from male to female, tetanus vaccination" -- the examiner cut her short.
"I was in good health otherwise," she said. "He said I would have to defer to the FAA and deferral is the correct thing to do. But he was curt with me, and I felt really, really awkward."
If Waterhouse had worked as a commercial pilot, the airlines could have helped with the costs and administration of the testing. Instead she said she was "just adrift."
Many of the commercial airlines and carrier services like UPS now have supportive services and antidiscrimination policies for their LGBT employees.
American Airlines helped veteran pilot Mark Feinmel when he became Melissa Feinmel.
When Feinmel had a sex change operation in 2000, American cleared many of the regulatory hurdles.
"There was a fear of losing my job, fear of losing my friends, fear of discrimination in the cockpit," she told Bloomberg Businessweek. American "helped [me] face all those issues," she said, allowing her to now fly 777s on trans-Atlantic routes.
As for Waterhouse, she tried talking to the FFA, "but you sometimes can't talk to the mountain," she said. So she took action.
Today, Waterhouse is ready to fly again. She still needs to submit medical documentation, but the biggest hurdle is now out of the way.
In the meantime, she has been working with a flight instructor on instrument rating and thinking about her next adventure. Ultimately, she wants to earn her commercial pilot's license.
"I love to fly, I love my motorcycle and I love my car," she said. "My next step is to learn how to sail."
Waterhouse said that as soon as she gets the medical certificate, she plans to take her boyfriend to lunch in the plane they have grown to love -- the Warrior II.
"I hope I've made a difference," she said. "It's hard to measure a thousand small steps, [but] it feels like there is a lot of progress we have made. It feels like the world is becoming a better place a lot faster."