I currently running a game that is very highly influenced but Naruto but is still using Pathfinder classes and monsters (Magic is called Chakra).
So just like the actual series, then? =p
As for your tags, seems a bit complicated for the effect, and are a bit off as compared to other Pathfinder items. I'd simplify it and clean it up a bit.
Explosive Tags: This is a sticky paper that can be applied to any object or surface as a Standard action that provokes attacks of opportunity. Priming the note is a Move action. The tag stays primed for 6 hours, after which is becomes inert. The tag can be detonated at will as a Swift action, dealing 1d6 Fire damage per tag level in a 5' radius burst, and allow a Reflex save for half damage (DC 10+1/2 the item's caster level). Tags that are subjected to Energy damage explode prematurely, though tags destroyed by other means, such as by being cut with a knife, are rendered harmless.
Special: This tag can be placed an a weapon. Upon striking the target the tag can be detonated as normal, the target taking the normal effects of the blast (including the Reflex save for half damage). If this tag is placed on a melee weapon and detonated, the wielder takes full damage as well, with no save.
I always just used them as a variant Alchemist bomb. Rather than chemicals in a flask, it's runes on paper, and modified by the delayed bomb discovery (mandatorily).
I had a ninja player who wanted to do this, but didn't want a level in the alchemist class, so I let him have it for a feat cost. I gave him a level 1 Alchemist bomb feature and then let him later take the remote detonate feat. Probably not a perfect balance, but it worked for our game.
Another alternative I might try, is make it a variation on Alchemist's Fire. I.E. the item from the core rulebook. Again, special effect change of tag instead of flask of goo, but same general effect.
That said, if you're going for a Naruto thing, it IS based of classic Japanese mythology. Traditionally they would use paper seals and charms for all sorts of spell effects (like a part of the casting costs).
All in all, they can be simulated fairly easily in a number of ways, through the basic rules and depending on how you want to do it. Personally, I think a combination of the above (i.e. change to a class feature by archetype or feat, feat access to the feature with limited per day uses simulating the amount one ninja can prepare for themselves, and "special" tags that cost more resources to prepare because they are a variant wondrous item/potion, maybe). Basically, whatever works in your game, and as long as everyone has fun.
There's already a ninja trick that lets you turn thrown weapons into projectiles. I always wanted to make a ninja magus archetype because I always thought they'd make the perfect naruto ninja.