This answer looks at Question 2, specifically the generalization to $n=3$.
Consider the problem of assembling a $3\times 3\times 3$ cube using a collection of $3^3=27$ cubies of $3^2=9$ colors, with $3$ cubies of each color, so that each color appears once on each face. There are four roles a cubie may play:
- a corner cubie contributes its color to three faces;
- an edge cubie contributes its color to two faces;
- a center-of-face cubie contributes its color to one face;
- the center-of-body cubie contributes its color to no faces.
Now each of the $9$ colors must appear on six faces. There are three ways to obtain $6$ as a sum of three numbers taken from $\{3,2,1,0\}$. They are $3+3+0$, $3+2+1$, and $2+2+2$. One of the nine colors must be used for the center-of-body cubie, so the other two cubies of that color must be diagonally opposite corner cubies (in order to have that color on all six faces). This leaves six other corners; since $3+3+0$ can only be used once, these remaining corners must each appear as part of the $3+2+1$ pattern, which means that each must be of a different color. This implies that the six center-of-face cubies must be of the same six different colors, as must six of the 12 edge cubies. There remain six edge cubies and two unused colors, which implies that the $2+2+2$ pattern must be used for the last two colors. That is, of the six remaining edge cubies, three are of one of the two remaining colors, and the other three are of the other remaining color.
Let the center-of-body cubie be of color $1$, and let the six center-of-face cubies be of colors $2$–$7$. We therefore start with the coloring
$$
\begin{array}{ccccccccccccc}
1&x&x&\phantom{x}&\phantom{x}&x&4&x&\phantom{x}&\phantom{x}&x&x&x\\
x&2&x&&&6&1&7&&&x&3&x\\
x&x&x&&&x&5&x&&&x&x&1
\end{array},
$$
where the first $3\times3$ square represents the front face, the second $3\times3$ square represents the middle layer, and the third $3\times3$ square represents the back face, all viewed from the front. We see that, for example, the center of the front face has color $2$, which implies that one of the corner cubies on the back face must also have color $2$. There are three possible corners; once a corner is chosen, then the edge cubie with color $2$ is uniquely determined. We may proceed in this manner to find many ways of assembling the cube. A few of these are below.
Assembly 1:
$$
\begin{array}{ccccccccccccc}
1&7&6&\phantom{x}&\phantom{x}&3&4&9&\phantom{x}&\phantom{x}&5&8&2\\
8&2&5&&&6&1&7&&&9&3&4\\
4&9&3&&&2&5&8&&&7&6&1
\end{array}
$$
Assembly 2:
$$
\begin{array}{ccccccccccccc}
1&7&6&\phantom{x}&\phantom{x}&9&4&3&\phantom{x}&\phantom{x}&5&8&2\\
8&2&5&&&6&1&7&&&4&3&9\\
3&9&4&&&2&5&8&&&7&6&1
\end{array}
$$
Assembly 3:
$$
\begin{array}{ccccccccccccc}
1&7&6&\phantom{x}&\phantom{x}&3&4&9&\phantom{x}&\phantom{x}&2&8&5\\
5&2&8&&&6&1&7&&&9&3&4\\
4&9&3&&&8&5&2&&&7&6&1
\end{array}
$$
These three are certainly not equivalent, even up to permutation of colors and rotation. To see this, observe that in the third assembly the corner cubie of color $j=2,3,\ldots,7$ on the face opposite the face on which color $j$ appears as the center-of-face cubie is always diagonally across from color $1$, but that this is true of only four of the faces in the first assembly, and of only two in the second assembly.
Added: Up to rotation, reflection, and permutations of colors, the three assemblies above are the only ones possible. The fact is proved and then used to give a complete enumeration below.
As above, we initially suppose that the center-of-body cubie is of color $1$, which means that two body-diagonally opposite corners, which we will take to be front, top, left and back, bottom, right, are also of color $1$. Denote these corners $a$ and $b$.
Two colors, which we will suppose to be colors $8$ and $9$, are used only as edge cubies. Let $E$ be the set of three edges on which color $8$ appears. The $12$ edges of the cube come in three parallel classes of four edges each. No face of the cube may contain two edges of $E$ since each edge of $E$ must contribute two new faces to the total of six faces on which color $8$ is to appear. Furthermore, $E$ cannot contain two edges that are parallel and across the body center from each other, since the two faces that are left without color $8$ are then opposite each other, and have no edge in common that would allow color $8$ to appear on both. Hence $E$ must consist of one edge from each parallel class.
The edges of $E$ will be incident on a total of six corners and nonincident on two, the latter of which are necessarily body-diagonally opposite. (If the two non-incident corners were opposite on a face, then that face would not contain color $8$; if they were joined by an edge, then the two edges parallel to that edge and opposite to it on the coincident faces would have to contain color $8$, an arrangement that we have already ruled out.) The set $F$ of edges on which color $9$ appears has the same properties. The sets $E$ and $F$ are, of course, disjoint.
There are now three possibilities for the incidence of $a$ and $b$ on $E$ and $F$:
- neither $a$ nor $b$ is incident on any edge of $E$ or $F$;
- each of $a$ and $b$ is incident on an edge of one set, say $E$, and nonincident on any edge of the other;
- each of $a$ and $b$ is incident on an edge of both $E$ and $F$.
In case 1, since the three edges incident on $a$ and the three edges incident on $b$ are not used in $E$ or $F$, the set $E\cup F$ consists of all six remaining edges, which form a $6$-cycle. The edge of this $6$-cycle will alternate between the colors $8$ and $9$, giving two possible edge $2$-colorings, one of which is shown.

After arbitrarily choosing one of the two possible edge $2$-colorings, say the one shown, and then arbitrarily assigning colors $2$–$7$ to the center-of face cubies, we have
$$
\begin{array}{ccccccccccccc}
1&x&x&\phantom{x}&\phantom{x}&x&4&8&\phantom{x}&\phantom{x}&x&9&x\\
x&2&9&&&6&1&7&&&8&3&x\\
x&8&x&&&9&5&x&&&x&x&1
\end{array}.
$$
We then find that the colors of all remaining cubies are forced, and the result is the third assembly above. As an example of this forcing: one of the three uncolored corners on the back face must receive color $2$. Whichever choice is made, we need to place one more cubie of color $2$, and it must be on an edge. Furthermore, the choice of edge is forced by the condition that every face contain the color $2$. We find that the color $2$ corner on the back face must be in the top left, since the other two choices would require the color $2$ edge cubie to be placed on an edge that is already occupied. Similar considerations force the placement of the remaining cubies of colors $3$, $4$, $5$, $6$, and $7$.
To enumerate the number of arrangements in this case, observe that we may color one face arbitrarily in $9!$ ways. We now need to decide which of the four body diagonals is to be the fixed-color one. Once this choice has been made, the rest of the arrangement is uniquely determined, giving $4\cdot9!$ arrangements.
In case 2, we choose one of the three edges incident on $a$ to be an element of $E$. The edge incident on $b$ parallel to this one cannot be in $E$, but one of the remaining two edges incident on $b$ must be chosen to be in $E$. The third element of $E$ is uniquely determined by these choices. We also find that the condition that no edge of $F$ be incident on $a$ or $b$ uniquely determines $F$ once $E$ has been specified. The edges of $E\cup F$ do not form a 6-cycle in this case. Instead, they form two disjoint paths of length $3$, one of which connects $a$ to $b$. An example is shown below.

In this example we chose to put color $8$ on the front-left edge, incident on vertex $a$, and then on the right-bottom edge, incident on vertex $b$. The color $8$ was then forced on the back-top edge. Since color $9$ is not to be placed on an edge incident on $a$ or $b$, the $9$ on the front-bottom edge is forced. The other two $9$s are then also forced. Arbitrarily assigning colors $2$–$7$ to the six center-of-face cubies, we have
$$
\begin{array}{ccccccccccccc}
1&x&x&\phantom{x}&\phantom{x}&x&4&9&\phantom{x}&\phantom{x}&x&8&x\\
8&2&x&&&6&1&7&&&9&3&x\\
x&9&x&&&x&5&8&&&x&x&1
\end{array}.
$$
The placement of colors $2$ and $3$ is then forced:
$$
\begin{array}{ccccccccccccc}
1&x&x&\phantom{x}&\phantom{x}&3&4&9&\phantom{x}&\phantom{x}&x&8&2\\
8&2&x&&&6&1&7&&&9&3&x\\
x&9&3&&&2&5&8&&&x&x&1
\end{array}.
$$
Color $6$ needs to be used on a corner of the right face, only one of which is not yet assigned. This then forces color $6$ on the back-bottom edge. Similarly, the placement of color $5$ is forced:
$$
\begin{array}{ccccccccccccc}
1&x&6&\phantom{x}&\phantom{x}&3&4&9&\phantom{x}&\phantom{x}&5&8&2\\
8&2&5&&&6&1&7&&&9&3&x\\
x&9&3&&&2&5&8&&&x&6&1
\end{array}.
$$
We now find that colors $4$ and $7$ can be placed in only one way, giving the first assembly above.
To enumerate the number of arrangements in case 2, observe that we may again color one face arbitrarily in $9!$ ways, and that we again need to decide which of the four body diagonals is to be the fixed-color one. Finally we need to choose among the six possibilities for the set $E$. Therefore in case 2 there are $4\cdot6\cdot9!$ ways of assembling the cube.
In case 3, we must choose the set $E$ as in case 2, but there are now three ways to choose the set $F$. (There are two ways to choose the edge in $F$ incident on $a$. If the chosen edge does not form a path with two edges of $E$, then the other two elements of $F$ are forced, as in the first picture below. If the chosen edge does connect two edges of $E$, then there are two ways to complete $F$, shown in the second and third pictures below.)



The first two of these are equivalent up to rotation of the cube; in these configurations, $E\cup F$ consists of two disjoint paths of length $3$. We find, however, that it is not possible to complete these configurations to a valid arrangement. For, taking the first one, we have
$$
\begin{array}{ccccccccccccc}
1&9&x&\phantom{x}&\phantom{x}&x&4&x&\phantom{x}&\phantom{x}&x&8&x\\
8&2&x&&&6&1&7&&&x&3&9\\
x&x&x&&&9&5&8&&&x&x&1
\end{array}.
$$
We must now put color $2$ bottom-left corner of the back face and color $3$ on the bottom-right corner of the front face. Then color $4$ is forced to go on the front-left corner of the bottom face, which is impossible since then color $4$ would also have to go on the back-right edge, which is already occupied by color $9$.
In the third configuration, the edges of $E\cup F$ form a $6$-cycle containing corners $a$ and $b$, a condition that uniquely determines $F$ once $E$ is specified. Since there are six ways to choose $E$, there are six such 6-cycles, but they are equivalent in pairs under interchange of colors $8$ and $9$.
The configuration shown gives
$$
\begin{array}{ccccccccccccc}
1&x&x&\phantom{x}&\phantom{x}&9&4&x&\phantom{x}&\phantom{x}&x&8&x\\
8&2&x&&&6&1&7&&&x&3&9\\
x&9&x&&&x&5&8&&&x&x&1
\end{array}.
$$
Color $6$, which must appear as a corner of the right face, can only go in the top-front corner. Likewise, color $7$ can only go in the back-bottom corner of the left face. Color $4$ must then go in the front-right corner of the bottom face and color $5$ in the back-left corner of the top face. The positions of colors $2$ and $3$ are then forced as well, giving the second assembly above.
To enumerate the number of arrangements in this subcase of case 3, once again we may color one face arbitrarily in $9!$ ways, and once again we need to decide which of the four body diagonals is to be the fixed-color one. Finally we need to choose among the three equivalence classes of $6$-cycles containing $a$ and $b$. Therefore in case 3 there are $4\cdot3\cdot9!$ ways of assembling the cube.
In conclusion, there are $4\cdot(1+6+3)\cdot9!$ arrangements of the $3\times3\times 3$ cube. For the $n\times n\times n$ cube, there seems to be a lot more flexibility when $n\ge4$, so I expect there to be many arrangements.