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Another question: How did you "crunch the numbers" on the Toxapex vs. Scizor substitute? Did you just try every logical option with the hp and spdef EVs? Or is there a math formula that I can input? Thank you for any responses
I get minimum EVs to be 64, which I verified to be correct. I'll bet you had level 50 numbers selected, not level 100 (it defaults to level 50 since it's primarily a VGC tool).

Regarding manual optimization: the easiest way is to just do it naively. Try doing it with only Sp. Def, then only HP, then with combinations of the two.