I would summarize the information as follows:
Development of the Sakae Model 31 progressed relatively smoothly at first, but in the autumn of 1944 the Japanese were confronted with numerous incidents of Zeros shedding their propeller blades. The problem was traced to weakness in the reduction gears installed. This affected approx. 300 aircraft in the A6M5 series. Personnel who had been working on Sakae 31 development were diverted to address this problem and, consequently, Sakae 31 development was suspended for some time. This spate of problems with propellers also coincided with the start of the Philippines campaign. As a result, the decision was made to install Sakae Model 21 instead in the new airframes. Some problems with the water-methanol injection mechanism were also encountered. So mass-produced Zero Model 52 Hei (A6M5c) used Sakae 21 (1,130 hp t/o) although it also had upgraded armament and protection. Therefore, overall average weight increased by nearly 3000 kg. Diving performance improved, but maneuverability and climb rate suffered significantly.
Development of the Sakae 31 later resumed, but was not completed until the beginning of 1945. Production of A6M7 took two parallel tracks. These were (a) Model 62 powered by Sakae 31 Ko and 31 Otsu (1,120 hp t/o) without water-methanol injection, and (b) what was designated as Model 63 powered by Sakae 31 which had been piling up waiting for completion of development tests. There was concern that the added weight of the water-methanol injection mechanism (100 kg) plus the associated 70 liter water-methanol tank would cause maneuverability to suffer. Consequently, the majority of the production effort focused on A6M7 Model 62.
Meanwhile, the Army's Sakae 31 development efforts (separate from the Navy's) proceeded smoothly and was achieved on a timely basis. A slightly modified version, the Sakae 32 (rated 1,300 hp t/o) was installed on the Type 1 Fighter Mark III (Ki 43 III) with production starting in July 1944.