We can take $H={\rm Sp}(4,3)$ to be the group $\{ A \in {\rm GL}(4,3) \mid AFA^{\mathsf T} = F\}$, where $$F=\left(\begin{array}{rrrr}0&0&0&1\\0&0&1&0\\0&-1&0&0\\-1&0&0&0\end{array}\right)$$ is the matrix of the preserved symplectic form.
The the matrix $$C =\left(\begin{array}{rrrr}1&0&0&0\\0&1&0&0\\0&0&-1&0\\0&0&0&-1\end{array}\right),$$ satisfies $CFC^{\mathsf T}= -F$, it normalizes and induces an involutory outer automorphism of $H$, and $\langle H,C \rangle$ is the conformal symplectic group, which I prefer to denote by ${\rm CSp}(4,3)$ (although it is sometimes written as ${\rm GSp}(4,3)$).
There are two dual 4-dimensional complex representations of $H$, which are interchanged by the outer automorphism induced by $C$, so this appears to be the automorphism that you are looking for.
From your description, I think the only possible structure of the group $G$ is the direct product $H \times C_3$.
To answer you specific questions, I am not sure what you are looking for in Question 1.
For Question 2, the full automorphism group group of $H$ is the image of ${\rm CSp}(4,3)$ mod scalars, which we can denote by ${\rm PCSp}(4,3)$: it has order $2|{\rm PSp}(4,3)| = 51840$. The involutory automorphism in question is an outer automorphism, and is not induced by an element of ${\rm PSp}(4,3)$.
For Question 3, I am not completely sure. There are actually two conjugacy classes of involutory outer automorphisms of $H$, one of which is induced by the matrix $C$ above, and I am not sure whether both can be induced by complex conjugation or only one of them.
An example of an element of ${\rm CSp}(4,3)$ that induces an involutory automorhism from the other class is $$C =\left(\begin{array}{rrrr}0&0&1&0\\1&0&0&-1\\-1&0&0&0\\0&1&1&0\end{array}\right).$$$$C' =\left(\begin{array}{rrrr}0&0&1&0\\1&0&0&-1\\-1&0&0&0\\0&1&1&0\end{array}\right).$$ This has order 4 in ${\rm CSp}(4,3)$, but its square is $-I$, so it induces an involutory automorphism. It is interesting that its centralizer in $H$ has order $720$, whereas the centralizer of $C$ has order $48$. That might be useful in deciding which automorphism is induced by complex conjugation.