EDIT 1. First part. We consider the orbit $O_A=\{HAH^{-1}|H\in G\}$ where $G=GL_l(p)$.
Assume that $p$ is a large integer and let $\chi_A$ be the characteristic polynomial of $A\in M_l(p)$ and $K=\mathbb{Z}/p\mathbb{Z}$. If $A$ is a random matrix, then, with a probability close to $1-\dfrac{1}{p}$, one has $discrim(\chi_A(x))\in K\setminus \{0\}$ and the eigenvalues of $A$ are distinct in $\overline{K}$.
Case 1. The eigenvalues are in $K$. Thus we may assume that $A$ is diagonal. We consider the stabilizer $G_A=\{H\in G|HA=AH\}=\{H|H\;diagonal,h_{i,i}\not= 0\}$. Then $card(G_A)=(p-1)^l$.
Case 2. The eigenvalues are not all in $K$. It is much more difficult! We seek the matrices $H=Q(A)=a_0I+a_1A+\cdots+a_{l-1}A^{l-1}$ (where $Q\in K_{l-1}[x]$) s.t. $\det(H)\not= 0$. We give two examples where $l=3,p=101$.
Example 1. $A=\begin{pmatrix}23&43&35\\98&20&64\\78&66&97\end{pmatrix}$ has $3$ distinct eigenvalues in $\overline{K}$ including one in $K$. $card(G_A)=101^3-10301=(p-1)^l+20000$.
Example 2. $A=\begin{pmatrix}98&40&79\\21&85&16\\44&4&91\end{pmatrix}$ has $3$ distinct eigenvalues in $\overline{K}$ and none in $K$. $card(G_A)=101^3-1$ ($\det(H)=0$ implies that $a_0=a_1=a_2=0$).
EDIT 2. Let $\chi_A$ be the characteristic polynomial of $A$. Using the Sedran's idea, we prove the following
Proposition 1. If $\chi_A$ is irreducible over $K$, then $card(G_A)=p^l-1$.
Proof. The eigenvalues of $A$ are distinct and algebraic of degree $l$ over $K$ and, consequently, are not roots of a polynomial of degree $l-1$. Thus $H$ cannot have a zero eigenvalue, except if the $(a_i)$ are zero.
Proposition 2. If $l\geq 3$ and $\chi_A(x)=(x-a)p_{l-1}(x)$ where $a\in K$ and $p_{l-1}$ is irreducible, then $card(G_A)=p^l-(p^{l-1}+p-1)$.
Proof. The eigenvalues of $A$ are distinct and, except $a$, are algebraic of degree $l-1$. If $H=Q(A)$ and $\det(H)=0$, then one studies two cases:
Case 1. $Q(a)=0$ that is $Q(x)=(x-a)q_{l-2}(x)$ where $q_{l-2}$ is an arbitrary polynomial of degree $l-2$; there are $p^{l-1}$ such polynomials.
Case 2. $Q(x)=\alpha p_{l-1}(x)$ where $\alpha\in K\setminus \{0\}$. There are $p-1$ such polynomials. $\square$
Finally $card(O_A)=card(G)/card(G_A)=\dfrac{(p^l-1)(p^l-p)\cdots(p^l-p^{l-1})}{card(G_A)}$.
Second part. Now I answer your question; you fix two similar matrices $A,B$. In fact, $card(S)=card(G_A)$. Indeed, if $U$ is a fixed matrix s.t. $UAU^{-1}=B$, then $S=\{UH|H\in G_A\}$.