EDIT: In addition, were scientific breakthroughs heavily stressed during the war effort of these two nations, or was the focus mainly on increasing wartime production?
The Japanese Type 93 oxygen torpedo, designed in the 30s, significantly outclassed any ship-mounted Allied torpedoes of the War. Torpedoes of the day generally used compressed air and fuel to flash water into steam in order to power a steam engine. The Japanese figured out how to safely and reliably use oxygen instead of air, which meant that the Type 93 was able to run without leaving a significant wake and could significantly outrange Allied torpedoes. The USN's Mark 15 torpedo had a maximum range of around 13,700 meters at 26 knots (the faster the torpedo is set to go, the lower it's range will be), whilst the Type 93 had a range of 40,000 meters at 36 knots. The Type 93 was a significant feat of engineering, and it served the IJN well throughout the war.
The emphasis placed by the Japanese on torpedo design stems from their doctrine, which advocated the use of torpedo-armed destroyers and cruisers in night battles that would wear down the US Pacific Fleet in order to reduce US strength before the decisive daytime battle between the IJN and USN. The actual course of the war did not follow the plans laid out by the Japanese, but the Type 93 nonetheless was able to inflict impressive losses on Allied warships.
Source: Kaigun by David C. Evans & Mark R. Peattie
The Japanese Government had one of the most advanced biological and chemical weapons programs known as the Unit 731 of the war which they used against Chinese Civilians. Even though Japanese scientists in the program carried out experiments on captured American POWs the US granted many of them immunity in exchange for handing over their research and continuing their work on behalf of the US Government, a similar deal to Operation Paperclip.