Based on actual holdouts in South East Asia from the Second World War from Japan. The last Japanese holdout from World War II was Hiro Onoda and was reached in 1974.
When Pam enters the Janitor's closet and uses the retinal scanner, the name that is shown when her identity is confirmed is "Shiro Kabocha". This is a reference to Drift Problem (2012) where Pam is drift racing. The Yakuza refer to her as Shiro Kabocha (white pumpkin).
When the Japanese soldier attacks Archer, Archer says, "Stop. Jesus, Kato, stop!" Beginning with the sequel to The Pink Panther (1963) (A Shot in the Dark (1964)), Inspector Clouseau (Peter Sellers) had an Asian servant named Kato (Burt Kwouk) who would attack him at unexpected times to keep the inspector alert and sharpen his martial arts skills. In the Pink Panther movies, Kato was Chinese. However, Kato in the Pink Panther series is an obvious homage to the role of Kato (Bruce Lee) in The Green Hornet (1966). Historically, Kato in the Green Hornet franchise (radio shows and movie serials as well as the TV series) started out as Japanese prior to World War II, when his ethnicity was retconned (first to Filipino, and later to generically Asian).
The cargo plane Archer is flown in on is a C-47, the military version of the DDC-3, painted with the WWII black and white 'Invasion Stripes', which were used to cut down on friendly fire incidents.
In the scene where Pam and Dr. Krieger meet in the Japanese bath, Krieger makes reference to Pam's pubic hair, which Pam describes as being shaped in the form of a lightning bolt with the letters "TCB", which she explains as standing for "Taking Care of Beaveness". This is a reference to Elvis Presley's personal monogram (also a lightning bolt topped with the letters "TCB" standing for "Taking Care of Business").