Kyoto – On a Wednesday morning in early April, a week after the launch of SoNoMa by SingleThread in Kyoto, Kyle Connaughton is reflecting on his lifelong relationship with Japan. Outside, cherry blossoms are blooming in the courtyard of the Capella Kyoto hotel , which houses SoNoMa in Miyagawacho’s historic kagai , or geisha district. A few minutes’ walk in either direction lie Kenninji, the city’s oldest Zen temple, and the venerable Kaburenjo theater, where Kyoto’s geiko (the regional term for geisha) performers still train. It’s hard to imagine a more storied Japanese address for an American chef to set up a restaurant. Connaughton rose to international prominence with SingleThread in northern California’s Sonoma County, a farm-to-table concept encompassing a restaurant and inn on the 24-acre farm run by his wife, Katina.…