Protocol means The formal etiquette and procedure for state and diplomatic ceremonies.
IHA means Imperial Household Agencies.
They say that the Empress can't step on the Emperor's shadow (well I think this applies to all female members of the Imperial Family, not sure if they need to do this even in private or only in the public).
Male needs to always walk first with the female members walking behind them (usually Princess Masako or the Empress gets off the car first and then they need to stand aside and wait for their husbands to get off and they usually bow to them the moment their husbands alight from their cars).
During press conferences the answers of Princess of the Empress' can't be longer than their husbands meaning that the male members should always be the one doing most of the talking (Masako was crtized during the engagement press conference for talking more than Naruhito....think it was 7 mins longer or something).
The Imperial family members usually align themselves according to the imperial succession line when they are in functions such as the garden party (like this order-Emperor, Empress, Crown Prince, Crown Princess, Prince and Princess Akishino, Prince and Princess Hitachi and etc.....).
The Imperial Family do not attend funerals of commoners, even if they are related. And the Emperor and Empress do not attend the funeral of lower-ranked Imperial Family members. Their chief chamberlain usually represents them.
When Imperial Family members give interviews on their birthdays or before leaving on foreign trips, all questions and answers are "screened" by the IHA.
The Emperor and Empress do not attend wedding ceremonies. If I recall it right, they didn't attend the wedding of Naruhito and Masako. The couple had the rites first then reported to the Emperor and Empress, who gave their blessing. However, they attended Sayako's wedding so I guess this protocol is no longer being followed or maybe they just insisted on being able to attend as the wedding marks Sayako's transition into a commoner.... not sure.
There are more certainly... but im not sure about it...