Short answers, pulled from the story.
American agents seized a set of codebooks bound in red covers from a Japanese naval attaché's luggage in 1923. This operation provided the first major intelligence on Imperial Japanese Navy communications and enabled Agnes Driscoll to crack the additive portion of Red Book code over three years.
Decryption efforts produced an intelligence report stating AF is short of water which confirmed that the main target of the Japanese Fleet was Midway Island. This information came from exploitation of JN-20 inter-island cipher systems during June 1942.
Codebreakers recovered large portions of the additive book used for encryption only two weeks after its introduction in April 1943. This breakthrough provided specific details about Yamamoto's flight schedule and route allowing United States forces to execute Operation Vengeance one year after the Battle of Midway.
British, Australian, Dutch and American agencies co-operated on breaking JN-25 well before Pearl Harbor through organizations like Station CAST and the Far East Combined Bureau in Singapore. Most credible sources agree no more than ten percent was readable at the time of the attack in December 1941.
In June 1942 the Chicago Tribune published an article implying U.S. Navy knew about Midway attacks beforehand based on information received by reporter Stanley Johnston. The government considered prosecuting the publication under the Espionage Act of 1917 but dropped charges following a grand jury investigation.