^If you're using him in the main game, don't bother with EVs or IVs, period. Unless you're doing an extremely limiting challenge run, any IVs are good enough for in-game, and EV training before the post-game sucks the fun out of playing really fast. You can spend the time looking for a decent nature (or at least, one that doesn't hinder Attack or Speed), but the hours you need to grind away for IVs are a complete waste of time.
Also, why do you have both Dark Pulse and Night Slash on the same set? Redundant coverage from different sides of the attacking spectrum, why? That's a beginner's mistake. Use one, drop the other. Sure, you'll meet some Pokémon whose defensive specialization means your chosen move will hit for lower damage, but you have other moves to hit those with.
I'd drop Toxic Spikes too. To set them up fully, you need two full turns, which you could better spend KO-ing two of the opponent's Pokémon. You're doing a solo run, which means your Greninja will be massively overlevelled, so there's little need to rely on passive damage. Besides, what are you gaining by using it? The only trainers with more than four Pokémon are the Champion and the Magikarp Fisherman. At most, you're spending those two turns Toxic-ing three Pokémon, and you'll be KO-ing them long before the Toxic damage starts paying off anyway. If you want to poison something, just use Toxic.
Lastly, I'd reconsider Hydro Pump. It has 5 PP, and an accuracy that wastes every 5th move in the long run. That's FOUR Pokémon you'll be hitting with your extremely useful Water STAB before you have to backtrack to a Poké Center to replenish PP. Use Waterfall or Surf instead, depending on whether you need a Physical or Special move. At any rate, don't go for Hydro Cannon either. It's a two-turn move, and most Water moves stronger than Water Pulse will outdamage it over two turns. Hydro Cannon is nifty to have when you want to finish your foe's last Pokémon quickly, but that's too situational to waste one of your only four moveslots on. Besides, in a solo run you'll be so overlevelled that you'll never really need the extra power that comes with Hydro Cannon anyway. In a sense, every move will be your finisher move when you're level 80 and the opponents barely brush the lower 50s.
Overall, I'd go for something like this:
- Surf (ranged/finishing move)
- Shadow Sneak (intercepting)
- Dark Pulse (ranged) OR Night Slash (intercepting)
- Ice Beam (ranged)
Drop either Dark Pulse or Ice Beam for Substitute if you want a non-damaging move.
As for your hold item... anything but Focus Sash, really. Focus Sash is useful when your foe is strong enough to KO you from full health. This will almost never happen in a solo run. Either, you'll have taken some damage beforehand, and Focus Sash won't activate, or the foe's strongest move will take a lot of HP off you, but not KO you, and Focus Sash won't activate. Lucky Egg will be the most powerful hold item in the long run, but if you somehow struggle you could go for Expert Belt or something. Honestly, even Mystic Water gets you a long way.
Hope this was of help!