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It works, but I get the feeling you don't fully understand how EV's work yet. I would visit GameFAQS and check an EV FAQ in the Emerald board to get a good idea on what they are.
Try to use Sleep Powder / Thunder Wave on it, and then just slowly weaken it. I'd bring like 30 Ultra Balls to be safe, but I have never needed more than 5 for anything, maybe I am just lucky.
Just use anything. You already have Raichu for Wallace, and Swampert can really kill anything. Just get something that is fast and can kill stuff. Gardevoir and Swellow are both good choices.
I'm pretty sure that in GSC when you say, used Toxic on Raikou it would keep that status effect. I'm not sure if that carries over into RSE, but that could be helpful if you could slap a Sleep Powder on it.
EDIT - Yes it does carry over.
You can't expect to beat a Water/Ice type Pokemon in the Elite 4 with a Water Pokemon of your own. Try catching a Magneton, Zapdos or maybe even Pikachu to kill it.