Can you imprint a card with X in its mana cost on Isochron Scepter and cast it with X equal to zero?

Let's be precise. Isochron Scepter requires imprinting an instant card with mana value 2 or less. Under CR 202.3b, when a card with X in its mana cost is not being cast (i.e., it is in any zone other than the stack), X is treated as 0 for the purpose of calculating its mana value. So a card like Brainstorm (U) has mana value 1, but a card like Absorb Vis (5B) has mana value 6 even with X=0 — wait, that's not X. For a card like Burst of Speed — let's use a real X example: Earthquake is a sorcery so irrelevant, but Repeal (XU) has mana value 1 when X=0, so it CAN be imprinted.

So the answer depends on the specific card. If the non-X portion of the mana cost has a mana value of 2 or less, the card can be imprinted (since X=0 in all zones except the stack per CR 202.3b). If the non-X portion alone exceeds 2, it cannot be imprinted.

When you activate Isochron Scepter to cast the imprinted card, you cast a copy of it. Since X instants cast this way are cast without paying their mana cost, and X is chosen as the spell is cast (CR 107.3b), X must be chosen as 0 — you pay no mana for the copy, so the only legal choice for X is 0 (CR 601.2b, 107.3b).

Concrete example: You imprint Repeal (mana cost XU) on Isochron Scepter. In exile, X=0, so its mana value is 1 — legal to imprint. When you activate the Scepter, you cast a copy of Repeal without paying its mana cost; X must be 0, so Repeal returns a permanent with mana value 0 to its owner's hand. It works, but X is locked at 0.

In summary: a card with X in its cost can be imprinted if its mana value with X=0 is 2 or less (CR 202.3b). When cast via the Scepter, X will always equal 0 because you are not paying any mana for the spell (CR 107.3b).