Mind Grind’s converted mana cost when it’s on the stack is 2 plus the value paid for X. (Mind Grind’s converted mana cost when it’s in any other zone is 2, but that doesn’t matter here.) If you counter Mind Grind (X = 4) with Mystic Genesis, the token will be 6/6.
Guile’s replacement effect means Mind Grind is exiled instead of being countered, so that part of Mystic Genesis’s effect will be replaced. However there is no “If you do” clause connecting the rest of Mystic Genesis’ effect to the spell being countered, so even though it’s not being countered by Mystic Genesis, so you’ll still get to make an Ooze token based on Mind Grind’s converted mana cost. (This is also true if you cast Mystic Genesis targeting a spell that can’t be countered, such as Supreme Verdict — Mystic Genesis will try to counter the spell but can’t, and then you’ll get your Ooze token anyway.)
Now as far as the rest…
If Mind Grind is exiled with Guile, it will forget all choices made for it, including the value paid for X. Then the player will have the option to cast the exiled Mind Grind for free… except they can’t. Typically, any time you cast a spell with X in its cost without paying that cost, the new X = 0. However Mind Grind’s text says “X can’t 0,” which prevents it being cast this way. The ruling on Mind Grind’s Gatherer entry clarifies this point:
If another spell or ability instructs you to cast Mind Grind “without paying its mana cost,” you won’t be able to. You must pick 0 as the value of X in the mana cost of a spell being cast “without paying its mana cost,” but the X in Mind Grind’s mana cost can’t be 0.
In other words, you can’t legally cast Mind Grind without paying its mana cost, because the “X can’t be 0” clause prevents it from being cast this way. If an effect (such as Guile’s) allows or forces a player to cast Mind Grind without paying its mana cost, they won’t be able to. (This doesn’t cause Guile’s ability to be countered, however — the rest of the ability, including exiling the spell, will still take effect.)
Finally, I want to make it clear that there is a difference between “You can’t cast this spell” and “Counter this spell.” The fact that you can’t cast Mind Grind for free doesn’t mean it counters itself — it means it never gets cast that way in the first place.
Effects which counter spells (including if the spell counters itself) explicitly say so in their text. (See Brain Gorgers, for example.) This is not the same as not being able to cast the spell in the first place.