Damn right he lost. Although neither Bruce or WJM were really injured at all after the fight. It actually ended after Bruce couldn't go on with his futile attacks any longer. Supposedly he was "unusually winded." Of course, it was after the fight that Bruce decided that Wing Chun was incomplete and he began to develope his own style. Linda Lee's bunk story about the fight came out well after Bruce's death. She spread a false story about the reason for the fight (the right to teach the quilo) and made up some crap about why Bruce decided to renounce his style. Jack Man Wong tried to defend himself in court for defamation of character but he lost since he was supposedly a "public figure."
Bruce actually never talked about this fight while he was alive. He made a vague reference to some "kung fu cat" he had fought in San Francisco. Everyone in Chinatown thought he was referring to WJM since it was well known that they had fought. Wong then challenged Bruce to a public match. Bruce Lee, remained silent to this challenge. He was probably afraid of being humiliated like he was in the first fight. After all, Wong managed to lock his head under his left arm three times.
If they had fought 5 years later the result would have been no different (the only difference might have been that Wong would've accidentally killed him). Wong grew in power and skill at just as fast a pace as Lee after their first encounter. He excelled in Ba Gua, Hsing Yi, and Tai Chi. He probably still would have won if he had used his Norhern Shaolin (he was a Bak Siu Lum grandmaster).
As far as Lee's supposedly superior physique, you might want to check out this link... http://www.myodynamics.com/articles/bruce.html