Alright, I am going to systematically begin reviewing your ideas at a hopefully acceptable pace.
Firstly, I'll ask that you add cooldowns (CD) to your ideas in the future. It makes it much easier to tell whether something is balanced or not. For now, however, I shall give you the benefit of the doubt that you balanced them well according to a CD and just forgot to include the CD; and so I'll review the ideas as they are.
The lore for this hero is intriguing but confusing. You said multiple times in the paragraph that he was tainted by evil, but at the end you contradicted those statements. So, which is it; is he tainted or no? I'm tending to lean toward the former, since his title is "Tainted Ninja". Cool backstory, in any case.
Do any of Viper's abilities inflict a status poison effect, or do they just inflict immediate True Damage? Aesthetically speaking, I would prefer the status effect. Balance-wise, however, I can see some difficulty in properly being able to construct his abilities while implementing the concept, so I would understand the decision of not including the status effect.
Snakeblade's statistics are totally balanced, excepting his damage output with the aid of Tainted Weapon. His damage per attack reaches 72-87 with the upgrade, and a goodly portion of that being True Damage to boot. That combined with the fact that he has a Fast attack speed (generally 0.5s) is OP. His DPS inasmuch as his base damage and this upgrade is 144-174, split between normal and True Damage. That's ridiculous: to nerf this, his attack speed should either be decreased to Average attack speed (1s) while lowering his armor to low to compensate for his insane DPS, or you should just decrease his base attack damage numbers and/or the upgrade's damage increasing numbers.
Shuriken Throw is balanced if its CD is in the realm of 8-10s. Besides that, I have nothing more to say on the subject of Shuriken Throw, since it is relatively simplistic.
Personally, I dislike this ability (Snake Fury) since it is so strikingly (no pun intended) similar to Kutsao's Leopard Style. It you would give the ability a makeover that is more related to snakes, then I would probably like it a lot more. (I recommend some sort of unique single target attack, though you may have something better in mind, so just have at it.) As it is, a 15-16s CD would be sufficiently balanced.
I like Serpent Counter (SC), but it would be cooler if you added a poison status effect to it for a bit of aesthetic flair. SC is relatively balanced as is, but the chance to counter should be the same as the chance to dodge. If you decide to implement a poison status effect, however, then it would be balanced with these numbers plus the poison DoT.
Does Viper have to be alive to perform this Hero Spell? If so, then that would be strange, as no other HS works like that for obvious reasons. Ignoring that, the HS is balanced with a CD of 60-70s. It would be more interesting (to me, at least; this doesn't mean that it needs this drastic of a change if you don't want to change it) if it dealt an initial 180 True Damage while inflicting 10 Poison DPS for 10 seconds to each enemy that it came into contact with, though. Cool HS as is, albeit quite similar to Arivan's.
I like the quotes that you gave him; they seem to fit his personality.
Overall, I really like Viper Snakeblade's concept as a hero and his powers for the most part. But he can do with improvement, which is true of almost any Fan Fiction idea. From reading your ideas, Valcedon, I can see that you are creative, so I look forward to reading the ideas of yours that I haven't yet had the privilege of viewing.
"Grammar is the logic of speech, even as logic is the grammar of reason." ~ Richard Chenevix Trench
"You don't have good grammar when you type with your fists." ~ C. F. Payne
valcedon 
