Question 1: Putting both curves in say, Legendre Normal Form (or else appealing the lefschetz principle) shows that if the two curves are isomorphic over $mathbf{C}$ then they are isomorphic over $overline{mathbf{Q}}$. Now we could say that for instance $E_2$ is an element of $H^1(G_{overline{Q}}, Isom(E_1))$ where we let $Isom(E_1)$ be the group of isomorphisms of $E_1$ as a curve over $mathbf{Q}$ (as in Silverman, to distinguish from $Aut(E_1)$, the automorphisms of $E_1$ as an Elliptic Curve over $mathbf{Q}$, that is, automorphisms fixing the identity point). However, $E_2$ is also a principle homogeneous space for a unique curve over $mathbf{Q}$ with a rational point, which of course has to be $E_2$, so the cocycle $E_2$ represents could be taken to have values in $Aut(E_1)$. Now $Aut(E_1)$ is well known to be of order 6,4 or 2 depending on whether the $j$-invariant of $E_1$ is 0, 1728 or anything else, respectively. Moreover the order of the cocycle representing $E_2$ (which we now see must divide 2, 4 or 6) must be the order of the minimal field extension $K$ over which $E_1$ is isomorphic to $E_2$. So $K$ must be degree 2,3,4 or 6 unless I've made an error somewhere.
Question 2: If you restrict your focus to just elliptic curves, yes your idea is right. If it's a quadratic extension, you have exactly 1 non-isomorphic companion. If you have a higher degree number field, you have nothing but composites of the quadratic case unless your elliptic curve has j invariant 0 or 1728.
Notice I am very explicitly using your choice of the word elliptic curve for both of these answers.
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