True, true. There were but two bomber groups in the South Pacific Theater that operated B-17s, the 19th and the 43rd. The 19th had been in action since the beginning and with arrival of the B-24 equipped 90th Bomber Group, was rotated back to it States. The B-24 proved superior to the B-17 due to its designed long distance over water capability. The in-theater 43rd Bomber Group transitioned to the B-24 by mid-1943, and USAAF B-17s in the Hawaiian Sea Frontier command were replaced By B-24s shortly after Midway as well, and that was the end of B-17 deployments in the Pacific. No, B-17s did not operate over the Japanese home islands at any point in the war. For the bare-bones presentation on the B-24 supplanting the B-17 in the Pacific and CBI theaters see https://warfarehistorynetwork.com/2017/06/30/boeing-b-17-flying-fortress-vs-the-consolidated-b-24-liberator/ In addition to the long-range reconnaissance missions for the USAAF, the USMC and the USN operated the PB4Y, the naval version of the B-24, in long range patrol and photo-reconnaissance missions.
Late edit, now that I think a bit more, Add that the only B-17s flying over Japan during the war were being flown by the Japanese. They had three of them, one pieced together from pieces-parts from wrecks in the Philippines and two captured intact in Java.