There were more B-29s lost to engine fires and other problems than to the Japanese. While the subs did a remarkable job of cutting off the supply line to Japan the B-29s mined many harbors with good results. In fact, the longest B-29 combat mission was dropping mines. The B-29s were an extremely valuable asset. Before Lemay changed the maintenance protocols for the B-29 engines several were lost on takeoff. They had to have max power on all 4 engines to make takeoff possible. The engine cooling cowl flaps had to be closed because of the drag they caused. Due to the ambient air temps I'll wager the engines ran a bit hot. The R3350 compound engines were radical for the time and produced a lot of power for the size. Like anything pushed to the limits there was a price. All of the accessory cases (pumps and generators) were made of magnesium and if an engine fire occurred and the magnesium ignited there was no putting the fire out and behind the front wing spar were the fuel tanks. The cowl flaps for engine cooling were quite large and if stuck open caused too much drag in flight. So much drag they couldn't make it back to home bases. Iwo was the midway point for the bombing campaign and the bombers were the only option to bomb the home islands until Iwo was taken. The navy put a picket line of subs to rescue downed B-29 crews that had to bail out or ditch. Taking Iwo likely released several subs for combat action. Like already posted, the plan to nuke Japan wasn't known.
