Keep in mind that as a carrier based naval fighter, the Zero was not commonly used to intercept B-29s. The primary Japanese interceptors would be the Nakajima Ki-43, Ki-44, Ki-63, and Ki-84.
The 43 was the Japanese Army's most common land-based fighter, and could reach the B-29 although it struggled to do so. The later Ki-63 was notable for being the only inline-engined Japanese fighter and had superb speed, although limited high altitude performance and lightweight armament meant it still had difficulty in intercepting B-29s. The Ki-84 was the best Japanese interceptor by far, having both the performance and the heavy armament to be a very serious threat to B-29s.
Edit: I forgot the Ki-44, which was the best *early* Japanese interceptor and was the only early Japanese fighter that was built for speed and climb as opposed to agility-at-all-cost. It was produced in limited numbers in parallel with the Ki-43, and was replaced late war by the -84.