I'm not sure this is a complete answer to your question (in particular, I don't work out any examples), but I have a number of comments to make, which I hope will be helpful. Let me first point out that whenever we want to eliminate quantifiers, we can focus our attention on a very special case.
A primitive existential formula is one of the form $\exists x\, \bigwedge_{i<n} \varphi_i(x,\overline{y})$, where $x$ is a single variable, $\overline{y}$ is a tuple of variables (possibly empty), and each $\varphi_i$ is an atomic or negated atomic formula.
Claim: Suppose that every primitive existential formula is $T$-equivalent to a quantifier-free formula. Then $T$ has quantifier elimination.
Proof: By induction on the structure of formulas. It suffices to handle inductive steps for the boolean connectives $\land$, $\lor$, and $\lnot$, and the existential quantifier $\exists x$, since we can rewrite $\forall x$ as $\lnot \exists x \lnot$. In the base case, every atomic formula is already quantifier-free, and the induction steps for the boolean connectives are trivial. So suppose we have $\exists x\, \varphi(x,\overline{y})$. By induction, we can assume $\varphi$ is quantifier-free. Writing $\varphi$ is disjunctive normal form, we have $\exists x\, \bigvee_{j<m}\bigwedge_{i<n_j} \psi_{i,j}(x,\overline{y})$, where each $\psi_{i,j}$ is atomic or negated atomic. Since $\exists$ distributes over $\vee$, this is equivalent to $\bigvee_{j<m}\exists x\, \bigwedge_{i<n_j}\psi_{i,j}(x,\overline{y})$, and by hypothesis each primitive existential formula $\exists x\, \bigwedge_{i<n_j}\psi_{i,j}(x,\overline{y})$ is equivalent to a quantifier-free formula, so we're done.
Now when $T$ is $\mathsf{ACF}$, an atomic formula is equivalent to $p = 0$, where $p$ is some polynomial with coefficients in $\mathbb{Z}$, and a conjunction $\bigwedge_{i<n} p_i \neq 0$ is equivalent to the single negated atomic formula $\prod_{i<n}p_i \neq 0$. So every primitive existential formula is equivalent to $\exists x\, (p(x,\overline{y}) \neq 0\land \bigwedge_{i<n} q_i(x,\overline{y})= 0)$. The upshot is that on very general grounds, eliminating quantifiers for $\mathsf{ACF}$ reduces to something very close to the special case you ask about in your Question 1.
In both Question 1 and Question 2, you seem to only be thinking about sentences, i.e., formulas with no free variables. E.g., in Question 2, you say that you're working with "polynomial equalities involving integers and the bound variables". But quantifier elimination is much stronger than this: it applies to formulas with free variables as well (and in fact we need this for the induction argument above, to handle formulas with multiple quantifiers). That is, we are trying to come up with quantifier-free conditions on the variable coefficients of our polynomials to ensure that there is some solution to our system of polynomial equations and inequations. Other than omitting the free variables, your understanding in Question 2 is correct.
Now for Question 3: There are two ways to go to show that ACF eliminates quantifiers from primitive existential formulas.
The hard route is to give an explicit algorithm - this will inevitably involve some clever uses of the division algorithm in multivariate polynomial rings. It has been a while since I've been through a proof, but I don't recall any particular step standing out as the non-trivial one. It's just good old-fashioned hard work, you might say. Maybe others can say something more helpful. The Math Overflow question you linked to has a number of references to this approach.
The easy route is to use model-theoretic compactness. This approach is given almost any introductory model theory textbook. It reduces the problem to showing that if $F$ and $F'$ are sufficiently saturated algebraically closed fields (i.e., of uncountable transcendence degree over the prime field) and $k$ is a countable common subfield of $F$ and $F'$, then for any $a\in F$, there exists $b\in F'$ such that $k(a)$ is isomorphic to $k(b)$ by an isomorphism fixing $k$. And this is essentially obvious, breaking into two cases depending on whether $a$ is algebraic or transcendental over $k$, and using the fact that $F'$ is algebraically closed and contains elements transcendental over $k$.
The drawback of the compactness approach is that it is non-constructive, i.e., it proves that every formula has a quantifier-free equivalent, but it doesn't tell you how to actually find the quantifier-free formula. Henry Towsner has a very nice recent preprint in which he explains how to extract algorithms from proofs of quantifier elimination using the compactness theorem.