A cool class, certainly. Where'd you get the Jutsu names, BTW?
The class is definitely a bit more potent than it should be, IMHO. I'd replace the general martial weapon proficiencies with just proficiency in the short sword, and maybe remove Sure Strike. It'd still be kinda too powerful, but I'm not sure what else should be removed...... Perhaps instead, reduce its BAB to poor, but give it Sure Strike at 2nd-level, while giving them Improved Feint as a bonus feat (regardless of prerequisites) at 5th-level. Then maybe give them an ability later, maybe 7th or 11th level, adding their Intelligence modifier or something to their throwing weapon ranged attack rolls out to a distance of 30 feet or so. This might make up for their slight excess of power, without really crippling them in battle (though it would hamper them somewhat, they'd still have good accuracy with Sure Strike + Improved Feint for one melee attack per round). Maybe give them an ability at some level that allows them to feint in combat with the Bluff skill from a distance, the same distance as with their throwing weapon bonus. Maybe.
In any case, regardless of that stuff...... A few of the abilities should probably be shifted around a bit, or broken up a bit. Quick Draw should probably be moved down to 1st-level. I'd suggest switching the levels at which Uncanny Dodge and Trapfinding are gained. Maybe move Trapfinding to 7th-level, Uncanny Dodge to 9th, and Evasion to 11th. Perhaps switch the levels that Improved Initiative and Trapfinding are gained...... And I agree with the other posters, swapping out Improved Initiative for some ability that adds Int mod or Wis mod to Initiative would be more interesting. The Mastery ability should be split up a bit I think; move part of its benefit down to 10th-level, and another part to 17th-level, IMO. I'd put a minor part of the Mastery at 10th, and another minor part at 17th, so it's at least a bit gradual and not such a sudden mastery of some new fighting style.
Mahoujutsu could use a slight boost, while Shurikendo could use a slight weakening; I'd suggest upping Mahoujutsu's DC to +3 instead of +1, since it only affects 2 or 3 abilities anyway; Shurikendo should be limited to shurikens only IMO, otherwise it should instead be reduced to a number of attacks equal to 1/3 shinobi level, rounded up; I'd suggest removing Stunning Fist from Taijutsu, but I'm not sure; maybe just have it function as the normal Stunning Fist feat rather than the monk's improved Stunning Fist usage (monks get more uses per day and I think a higher save DC with it).
If spreading out the Mastery benefits, I'd suggest the following: 10th-level Mahoujutsu would be the 1st extra Quicken Spell-Like Ability feat, 17th-level Mahoujutsu would be the 2nd extra Quicken Spell-Like Ability feat, and 20th-level Mahoujutsu would be +3 to Jutsu DCs; 10th-level Shurikendo would be a number of throwing attacks equal to 1/4 shinobi level, at 3/4 base attack bonus for its throwing attacks, both rounded up, while 17th-level Shurikendo would be the same but at full base attack bonus for each attack, and 20th-level Shurikendo would be 1/3 shinobi level in throwing attacks, rounded up, at full base attack bonus for each attack; 10th-level Taijutsu would be Improved Unarmed Strike and the unarmed strike benefits of a 10th-level monk, while 17th-level Taijutsu would be the unarmed strike benefits of a 15th-level monk, and 20th-level Taijutsu would be unarmed strike benefits of a 20th-level monk, plus Stunning Fist if you keep that.
Them's my opinions, take 'em or leave 'em as you will. {:^D