First and foremost:
Iaijutsu abillity: Iaido is a skill of drawing a sword with extreme speed AND killing the opponent in one blow... Iaijutsu is the abilitie to draw the sword, kill the opponent and hack away at him for the next five minutes in a continuous effort, just in case the first blow doesn't kill him... So, any samurai characters that have a katana may draw her and get a free attack at their highest attack bonus.
Second:
The Kiai abillity:
As a kendoka, I came to realise that Ki is always usable and not only in special occasions and especialy not once per day... Try seven or eight times per thirty seconds... So I made it deal less damage... It is just damage + level, no charisma modifier.
Third:
The Daisho proficiency:
Not all samurai were trained in use of both Wakizashi and the katana at the same time. A lot of them used only the katana, so the two-weapon fighting feat has been removed and now must be taken as a normal feat.
Finaly:
A smaller risk has been introduced that is optional... I personaly rarely use it since it is a bit extreme....
The Shogun must always be present in every game where there is a samurai. Also, every now and then (At the DM's discression) a % die is rolled if the roll is 100%, that means that there is an attack on the Shogun. Now a d20 is rolled to see how many days will pass before a messenger from the Samurais town will come. All results under five are treated as five. The samurai must travel back to his town (same duration of days) and find the assassin of the shogun, kill the bastard and the may continue with the adventure...
-modification to the last-
If the DM chooses, there may be no shogun, but that the Samurai is called Ronin and he does not recieve the Katana or the wakizashi at the beginning of the adventure. He must find them thruout the game...
That's about it...