The Tennenbaum phenomenon is amazing, and that is totally correct, but let me give a direct proof using the idea of computable inseparability.
Theorem. There is no computable model of ZFC.
Proof: Suppose to the contrary that M is a computable model of ZFC. That is, we assume that the underlying set of M is ω and the membership relation E of M is computable.
First, we may overcome the issue you mention at the end of your question, and we can computably get access to what M thinks of as the
nth natural number, for any natural number n. To see this, observe first that there is a particular natural number z, which M believes
is the natural number 0, another natural number N, which M believes to the set of all natural numbers, and another natural number s, which M
believes is the successor function on the natural numbers. By decoding what it means to evaluate a function in set theory using ordered pairs, We
may now successively compute the function i(0)=z and i(n+1) = the unique number that M believes is the successor function s of i(n). Thus,
externally, we now have computable access to what M believes is the nth natural number. Let me denote i(n) simply by n. (We
could computably rearrange things, if desired, so that these were, say, the odd numbers).
Let A, B be any computably inseparable sets. That is, A and B are disjoint computably
enumerable sets having no computable separation. (For example, A is the set of TM programs halting with output 0 on input 0, and B is the set of
programs halting with output 1 on input 0.) Since A and B are each computably enumerable, there are programs p0 and p1 that
enumerate them (in our universe). These programs are finite, and M agrees that p0 and p1 are TM programs that
enumerate a set of what it thinks are natural numbers. There is some particular natural number c that M thinks is the set of natural numbers
enumerated by p0 before they are enumerated by p1. Let A+ = { n | n E c }, which is the set
of natural numbers n that M thinks are enumerated into M's version of A before they are enumerated into M's version of B. This is a computable
set, since E is computable. Also, every member of A is in A+, since any number actually enumerated into A will be seen by M to have
been so. Finally, for the same reason, no member of B is in A+, because M can see that they are enumerated into B by a (standard)
stage, when they have not been enumerated into A. Thus, A+ is a computable separation of A and B, a contradiction. QED
Essentially this argument also establishes the version of Tennenbaum's theorem mentioned by Anonymous, that there is no computable nonstandard
model of PA. But actually, Tennenbaum proved a stronger result, showing that neither plus nor times individually is computable in a nonstandard model of PA. And this takes a somewhat more subtle argument.
Edit (4/11/2017). The question was just bumped by another edit, and so I thought it made sense to update my answer here by mentioning a generalization of the result. Namely, in recent joint work,
we prove that not only is there no computable model of ZFC, but also there is no computable quotient presentation of a model of ZFC, and indeed there is no c.e. quotient presentation of such a model, by an equivalence relation of any complexity. That is, there is no c.e. relation $\hat\in$ and equivalence relation $E$, of any complexity, which is a congruence with respect to $\hat\in$, such that the quotient $\langle\mathbb{N},\hat\in\rangle/E$ is a model of ZFC.
Question 2 is an immediate consequence of the compactness theorem. Let $\kappa$ be fixed, and for each $\alpha < \kappa$ add a constant symbol $c_\alpha$ to the language. Add axioms of the form $c_\alpha < c_\beta$ for every $\alpha < \beta < \kappa$. The new theory $T$ is finitely satisfiable (every finite fragment is interpretable in the standard model of PA). So $T$ it is satisfiable, and the map $\alpha \mapsto c_\alpha$ is the desired embedding.
For question 1, it is known that $D$ cannot have the order type of the reals. There is a nice survey by Bovykin and Kaye [1] that includes this fact and has a lot more information about order types of models of PA. In the comments below, Andrey Bovykin suggests downloading his thesis from his homepage [2]; the paper is a summary of parts of the thesis.
1: Bovykin, Andrey; Kaye, Richard. Order-types of models of Peano arithmetic. (2002) Logic and algebra, 275--285, Contemp. Math., 302; MR1928396, DOI: 10.1090/conm/302/05055, http://www.maths.bris.ac.uk/~maaib/orders.ps
2: https://logic.pdmi.ras.ru/~andrey/research.html
Best Answer
The answer to your question is no. For example, suppose $\kappa$ is inaccessible and $M = V_{\kappa}$. Then $M$ is a model of $\sf ZF$ but $M$ cannot be countable in $N$ as it is not countable in $V$.
Of course there will always be a set generic extension of $V$ containing such an $N$ (just generically add a bijection from $M$ to omega)