I assume $\phi_1=\pi_1$ ?
(i) The first question is really easy : $Hom(\pi_1(X),GL(\mathbb{C}^n))=Hom(\mathbb{Z},GL(\mathbb{C}^n))=GL(\mathbb{C}^n)$ because a morphism $\mathbb{Z}\rightarrow GL(\mathbb{C}^n)$ is entirely determined by the image of $1\in\mathbb{Z}$. This image is denoted $\alpha$ and is the monodromy operator.
If $\pi_1(X)\neq\mathbb{Z}$, then of course, we don't have such isomorphism. But for example, if $X=\mathbb{T}^2$ is a torus, $\pi_1(X)=\mathbb{Z}^2$ and $Hom(\pi_1(X),GL(\mathbb{C}^n))$ is isomorphic to the set of pairs $(f_1,f_2)$ where $f_1$ and $f_2$ are two commuting linear isomorphism of $\mathbb{C}^n$. ($f_1$ and $f_2$ are the image of the canonical basis of $\mathbb{Z}^2$).
For general $X$, the data of a local system is equivalent to a representation of $\pi_1(X)$.
(ii) Let $X=\mathbb{C}^\times$. A local system of rank 1 can be pictured as follow : for each point $x\in X$, imagine that we have a copy $F_x$ of $\mathbb{C}$ (with the discrete topology). These copies of $\mathbb{C}$ are not unrelated : if $U$ is a small disc in $X$, $x,y$ are two points in $U$, then we can identify $F_x$ and $F_y$. The identification can be pictured as follow : if $c:x\rightarrow y$ is a path from $x$ to $y$ in $U$, then for each $f_x\in F_x$, there is only one way to move from $f_x$ in the local system such that "we stay over the path $c$" (this is because $F_x$ is discrete !). We end up in $F_y$ to get an element $f_y$. The correspondence $f_x\mapsto f_y$ is the identification (it doesn't depend on the choice of the path $c$).
But what happen if I take two points $x,y$ not closed to each others ? We can take a path from $x$ to $y$, and we will have again an identification between $F_x$ and $F_y$. But this time, this identification will depends on the choice of the path (at least, two homotopic paths will give the same identification).
So if I take a loop based at $x$, I will get an automorphism of $F_x$, this isomorphism may not be the identity ! This is the monodromy along the loop. It is an important fact that the monodromy along every (up to homotopy) loops characterize the local system.
On $\mathbb{C}^\times$, this is entirely determined by the monodromy around the origin, this is your $\alpha:F_x\rightarrow F_x$.
(iii) Let's see a concrete example. Let $F$ be the local system such that $F(U)$ is the set of solutions to the differential equation of $\frac{f'}{f}=\frac{1}{2z}$ on $U$. At a point $x\in X$, there is a bijection $F_x\simeq \mathbb{C}$ given by $f\mapsto f(x)$.
Note however, that if $x,y$ are two points in a small disk, the identification $F_x\simeq F_y$ is the following : let $f_x\in F_x\simeq\mathbb{C}$, let $f$ be a solution of $\frac{f'}{f}=\frac{1}{2z}$ on $U$ such that $f(x)=f_x$, then $f_y\in F_y$ is simply $f(y)$ through the identification $F_y\simeq\mathbb{C}$.
I am not sure I am very clear here (please tell me !).
Now I claim that if $c$ is a loop around the origin, the map $F_x\rightarrow F_x$ is the multiplication by $-1$. Indeed, the solutions of the differential equation on a small disk $U$ are the functions $C\sqrt{z}$ for a given choice of square root of $z$. But if we turn around the origin, we will get the opposite choice.