Well, with what I know, remember, my own experiences, and what I've read, let's see...
Hey guys, this is my first ninja ever so I have lots of questions about it. 
So let me start them... 
1.) So I know Throw Kunai is not so OP as it used to be but my level 31 ninja using some Poison Kunais has about 800 damage at orc village. My weapon is a +8 stilleto and I don't know what I should do to improve the damage because 800 is like a Bash of a swordsman... lol.
Is Dagger Throwing Practice at 10? Sounds like it's at the minimum required if you're hitting for 800. Also better to have some Ice with you going into orc village. Usually when I leveled up I'd take Fire and Ice and switch off between them while hunting in Orc Village and Dungeon.
It's still...semi-OP, in that you can pull off considerable damage abusing element weakness.
Other than that anything that adds to Str or Equipment Attack. So Porcellio Card (cheapest method) in a +3 Str armour would be solid. Bloodied Shackled Ball + Shackles helps. So does The Sign.
You could add + Attack cards if you want to to your Stilleto. Better Knife options include a Grimtooth, which you're almost in range for (level 36 required), and a 3s Gladius (this is actually superior for now, at least if you can boost it with +atk cards or if you can afford AS cards easily, but frankly this would be a waste of AS cards). Any other equipment that adds to attack, and I know there are others but I can't think of anything. Evil Marching Hat if you can afford it, would offer the greatest return in overall damage boosting performance for Kunai and later on, Kunai Explosion.
Ensure you maximize Strength, since I'm pretty sure iRO still favours Kunai as an "always hit" skill that goes off Strength for damage, so Dex should have little use beyond adding extra damage, for now anyway.
2.) My skill tree would be something like this:
Is it a good one? What should I do to improve it?
Eh, it's different for sure. Kagerou points into Ninja skills? Plus you're aiming for both auto-attack and throwing skills? That's a bit too spread out to be truly effective. This is especially bothersome when Right/Left hand mastery has NO effect on skill damage. You also have Throw Coin, which to my knowledge is not necessary to max to get anything out of Rapid Throw, and on its own has no practical use, being both expensively wasteful and extremely low damage per zeny. So it's only necessary for the prerequisites.
You're also sacrificing arguably the best defensive technique ever handed to a glass cannon, Illusion: Shadow. It's even better than Cicada since you don't have that annoying throw that puts you out of combat and often mucks up timing if your screen isn't properly showing enemy placement. I would say, no matter what build anyone makes, four skills are an absolute must for Kagerou and Oborou. Earth Charm [1], Illusion: Shadow [5], 16 Night [5], and Pure Soul [5]. That is 16 points, so job 17, of absolutes. Close to an absolute is Shadow Hiding [1], which SHOULD be in every build, but isn't necessary, especially for people who have a slotted The Sign of Hiding, or who don't mind switching out the first accessory slot at will.
Most effective builds go for focusing on one thing or another, and get alternative skills to add some flavour.
Basic cookie-cutters are WOE Damage (which is technically a PvP build, with Rapid Throw), WoE Support (nix the Rapid Throw, get the other WoE skills, but ensure to get Makibishi), Throw (Explosion, Petal, Splash), and that's really it.
Very few go for Melee. Soul Cutter is...meh, it can be useful, but it does not factor in Right/Left mastery, which only affects standard Attack. Cross Slash is slightly better, and can actually be very good, however this is ONLY at high levels and ONLY if you have a second Kagerou/Oborou with the skill and you get to hit second. So very situational.
The other problem is stats. Sure you can spread stats a lot going towards 150, but dual dagger is slow, meaning to make it remotely effective, you'll require double attack, and you'll require more Agility than is necessary for any other build, or necessary to make the most out of your character.
At least you can reset your skills, costs money or zeny, but you can experiment a bit. If you want I'll post after this with some general build concepts that work.
3.) My equipments so far are:
+9 Rideword Hat w/o card.
Robot Eyes.
Well Chewed Pencil.
+9 Heroic Backpack with Orc Baby Card.
I have a Calm Mind Huuma for the Swirling Petal quest but it is a equipment for the future... what should I get for now?
I don't have much money to spend now... something like 50m is my max this month, but next month probably I will buy some more KP...
Heroic Backpack works, but as I said above you'll want Bloodied Shackled Ball + Shackles and a Porcellio carded armor. Rideword is useful (I suggest a Carat Card, just for general use), but as with the above, Evil Marching is superior for this in every way, especially given Pure Soul. Robot Eyes are solid, as is Well-Chewed Pencil.
As with the above, Grimtooth or a Damascus. Though honestly, Eden Daggers provide enough damage still, especially Dagger III, to carry you easily with the other equipment, and while abusing element weaknesses, to Kagerou, even with the nerf to Kunai.
4.) Kagerous are like samurais, and samurais rock! But samurais are like... melee warriors... so, is melee kagerou worth it? Does it do a decent damage on pvp/woe?
Well...err, if Samurai gave up their sense of honour in direct combat, and switched their Samurai swords for Wakizashi and Kunai, then sure.
Going off this. Um, you know, it's not typical, but you should do what you think is fun. If you would actually prefer Melee, than choose a few throw skills you cannot do without, and go from there, and while Cross Slash isn't superb without a backup K/O for that first CS hit, it is still useful (just don't expect to kill in TI's with it). What are samurai without their accompanying solo versions, the Ronin, the warrior without a master.
Honestly I think you should have fun before anything else. What's the point of playing a game just for stats unless you know you have the time, money, and drive to be the absolute best?
If you really want a true Melee build, then you must have Shadow Warrior, since the only way to get any effectiveness out of Right/Left is by boosting your auto-attacking abilities, then Cross Slash, since you need some sort of attack that doesn't kill you, and deals more than Haze Slasher and Shadow Slash. You could also aim for Kunai Splash, since it takes from % cards that are Element/Race/Size based thanks to some testing, or go for Explosion which offers a lot more damage and still counts in those Element/Race/Size cards.
Realize that a true melee build will be pretty expensive. There is no general purpose backhand save for Turtle General Card (and a few upcoming cards on kRO that add % damage to everything), unlike with pure throw builds, so you must have a full set of Main Gaunches, and the closest to general will be specifically targetted weapons for particular maps, such as Orc Lady card for Orc based maps, Drainliar for Byalan and most of the other water-based dungeons. Or you could go Size cards.
Also realize that Right/Left mastery has no impact on your Huuma's damage, since it requires dual daggers to even trigger, and even if it did, again, it would only be for standard attack damage, not skill damage.
Here's one build concept:
http://irowiki.org/~...5qorA3rAaf1dnhf
Has some room for growth, just note the Ninja points should be considered for prerequisites first, then whatever is left over, put as you see fit.
Basically you can get Rapid Throw to max, and that takes up the rest. You could put points into Cross Cut and either Kunai Splash or Kunai Explosion, and the leftovers into Makibishi (very useful skill).
5.) For Kagerou leveling would it be necessary Hunterfly Cards on my Swirling Petal Huuma or some Archer Skeleton cards for damage since Kagerous have that skill which recovers lots of HP/SP per secod?
Well, that is it for now...
Thank you guys! 
NOOOO, Soul, again, is more than enough. Heck, it's the only class in the game that can keep itself at near full health at all points if you're fast enough to keep it up whenever possible.
Archer Skeleton cards for damage if you're going to use a Swirling Petal.
