Pokemon Y
Nature: Modest

This is my first time looking at IV's so I may be reading the numbers on the right incorrectly. Are my 31 IV's HP, ATK, and SP. ATK good?

Or should I soft reset again?

well those are good
but also be aware unbreedable pokemon such as mewtwo always have 3 31 IVs now

Minimum 3 perfect IVs

personally I would reset, since the other 3 are very very low. And speed is pretty important.

Ideal would be something like 31 HP, 31 Sp. Atk, 31 Speed as Modest if you want normal Mewtwo/MegaTwo