Magic Damage and Spell Damage are Different!

Currently it says wands increase Magic Damage by a percentage. That's wrong. +Magic Damage% bonuses, such as the Crown Ice Wand, and the Magic Mastery Title, are different from what's here, which are increases to your INT bonus. According to the JP wiki, the formula is roughly (Base damage + wand) * (Int bonus + Element Mastery Bonus + Element Mastery Title + Bolt Mastery Bonus*Bolt Mastery Title)*(Magic damage% bonuses)*1.1

The stat here would add onto your int bonus, not your magic damage% bonus.

The damage is (Base Damage + ((Wand + Enchant)*Spell_Modifier_Constant) * (1+INT/2000) * (Wand + Wand_Over_Upgrade) * (Element_Mastery_Bonus) * (Bolts_Mastery_Bonus) * (Title_Modifier).

No it's not. Those bonuses don't multiply together. Check the JP wiki. http://mabinogi.wikiwiki.jp/index.php?%A5%B9%A5%AD%A5%EB%2F%CB%E2%CB%A1. And I apologize. I was wrong about special upgrades. They actually just add +9 to the spell's base damage after protection, but before masteries and +magic% bonuses.

Here's the JP wiki's sample calculation for a Fireball with +9 magic damage from Special upgrades, a phoenix fire wand with -6% damage, 30 magic attack (i.e. 600 INT), and all magic skills at rank 1. The defender has 10 prot, and no defense or mana reflector.

スキル[ファイアボール] チャージ[5] 武器[フェニックスファイアワンド] ダメージ[-6%]

特別改造S[0] -- 2400*(1-0.1)*(1+30/100+0.15)*(1-0.06)*1.1 = 3238

特別改造S[9] -- (2400*(1-0.1)+9)*(1+30/100+0.15)*(1-0.06)*1.1 = 3251

Notice the Fire mastery bonus (0.15) is added onto the int bonus, and the S type upgrade bonus (+9) is added onto the base damage

Well JP server might be that way. But on KR it gives a % bonus. In the patch notes for G13S2 there was one that said that the Special Upgrades for wands and staffs was typod and was supposed to be a %. And since then it has shown up as such. Considering I play on KR and that is how I've observed the damage, that is what I believe it to be. You should also be aware that the JP server is a deviant when it comes to patches and is different than the other versions of mabinogi.