Let me treat the case where the
underlying set is infinite. These answers reveal that the
question is likely to be much more interesting in the finite case, and
so it should probably be regarded (and perhaps re-tagged) as a
question of finite combinatorics.
In the infinite case, your cardinal $\beta$ is either $0$
or equal to $\alpha$, depending on whether all points are
equivalent or not. The reason is that if the relation is
not trivial, then every point is inequivalent to some other
point, so $\alpha\leq\beta$, and conversely
$\beta\leq\alpha\cdot\alpha=\alpha$ by infinite cardinal
arithmetic.
For question 1, the answer is therefore that $\kappa$ is
not determined by $\alpha$ and $\beta$. As you observed,
$\kappa$ is the number of classes, and the same infinite
set of size $\alpha$ can be partitioned into any number
$\kappa$ of classes, provided $1\leq\kappa\leq\alpha$.
For question 2, when $\alpha$ is infinite, then since
$\beta=\alpha$ (unless there is only one class, in which
case $\beta=0$), the bound $\gamma$ is not very helpful. But the largest $\kappa$ can be is $\alpha$. (This is under AC; without AC, then it is possible that $\kappa$ could be strictly larger than $\alpha$, as I expain at the bottom.)
Similarly, for question 3, the smallest $\kappa$ can be is
$1$, when $\beta=0$, and otherwise, $\kappa=2$ is possible,
since you can divide $\alpha$ into $2$ classes, each of
size $\alpha$.
Finally, let me mention that there are some interesting
issues that arise with the Axiom of Choice in this
question. Your observation that the quotient has size
$\kappa$ seems to rely on AC, since the chains are
essentially choice functions. More generally, it was
observed in a previous MO by Dr. Strangechoice that
$\kappa$ can actually be strictly larger than $\alpha$! For
example, consider the relation $E$ on the reals, where
$xEy$ if $x=y$ or if both $x$ and $y$ code a well order on
the natural numbers having the same order type. This is an
equivalence relation on the reals, but it is consistent
with ZF that there is no $\omega_1$-sequence of reals, and
in this case there can be no injection from the $E$-classes
into the reals, since this would provide such an
$\omega_1$-sequence. But there is a converse injection,
since we can injectively map reals to reals that don't code
well-orders. So this is a situation where the number of
equivalence classes is a strictly larger cardinality than
the underlying set.