Ariyan,
EDIT: This contains some substantial edits and added references.
Lipman has defined the following notion (EDIT: twice):
Definition (Lipman ; Section 9 of "Rational singularities with applications to algebraic surfaces and factorization"): If $X$ is 2-dimensional and normal, $X$ has two pseudo-rational singularities if for every proper birational map $\pi : W \to X$ there exists a proper birational normal $Y$ over $W$ where, $R^1 \pi_* \mathcal{O}_Y = 0$
Definition (Lipman-Teissier ; Section 2 of "Pseudo-rational local rings and a theorem of Briancon-Skoda about integral closures of ideals"): $X$ has pseudo-rational singularities if $X$ is CM (Cohen-Macaulay) and if for every proper birational map $\pi : Y \to X$ with $Y$ normal, $\pi_* \omega_Y = \omega_X$.
If these are the same in dimension 2, this seems pretty close to what you want in dimension 2.
EDIT2: These are the same in dimension 2, I was in Purdue and asked Lipman about question 1, which holds, and certainly implies this.
He also points out that regular schemes are pseudo-rational. In particular, this implies that if $\pi_* \omega_Y = \omega_X$ for one resolution of singularities, it also holds for every resolution of singularities (in fact, for every proper birational map with normal domain).
In dimension 2, he also studies relations between this condition and the local-finiteness of the divisor class group.
On the other hand, I'm pretty sure this is different from the definition of rational singularities you gave above at least in higher dimensions (with the appropriate $R^i$ vanishing instead of just $R^1$).
With regards to your specific questions:
Question #1: That vanishing, called Grauert-Riemenschneider vanishing, is known to fail for $\dim X > 2$ outside of equal characteristic zero. I believe the answer should hold in the two-dimensional case, certainly it should assuming that Lipman's various definitions of pseudo-rational singularities are consistent.
EDIT: This holds in dimension 2, see Theorem 2.4 in Lipman's "Desingularization of two-dimensional schemes".
In any dimension, that vanishing has recently been proven in equal characteristic $p > 0$ over a smooth variety (or a variety with tame quotient singularities), see arXiv:0911.3599.
Question #2: In higher dimensions, I'm pretty confident that the answer is no. In the 2-dimensional case, probably this is done by Lipman? In view of question #1, in order to find such a counter example in higher dimensions, one should look at various cones probably over 3 or 4-dimension schemes with negative Kodaira dimension (probably Fano's) but which fail Kodaira vanishing.
I have some thoughts on some other definitions of rational singularities which might be better in mixed characteristic, but I'm not sure I want to post them on MathOverflow right now. If you email me, I'd be willing discuss it a bit.
Quotient singularities can behave a little different outside of characteristic zero as well (see various papers of Mel Hochster from the 70s for instance). This can also lead one to look at questions like the Direct Summand Conjecture.
A subtlety here is that I don't think the second arrow in your short exact sequence is not supposed to be canonical. (It's not canonical in general, and I don't think the data of $\tilde{X} \to X$ is enough to make it so.) It is if $\tilde{C}$ is a reduced divisor, by the residue map, but that's probably not relevant here.
So one has the short exact sequence
$$ 0 \to \tilde{\mathscr C} \to \mathcal O_{\tilde{X}} \to \mathcal O_{\tilde{C}}\to 0$$
by definition.
Question: What invertible sheaf can we tensor the first term of this exact sequence by to get the first term of the desired short exact sequence?
Question: What happens to the second term if we tensor by the same invertible sheaf?
Question: What happens to the third term if we tensor by the same invertible (and thus locally trivial) sheaf?
For Q1, it is as Mohan says in the comment — it is a local question, and you can use local rings.
For Q3 it just means that for $I$ the ideal sheaf of a divisor $D$ and $L$ any line bundle, a section of $L \otimes I^{-1}$ gives a section of $L$ over the open set $\tilde{X}-D$, i.e. a meromorphic section of $L$. If we choose a local generator for $L$ at a point of $D$ and express this section as a rational function times the generator, the rational function may have a pole at that point (since it's not a section over that point) but the order of the pole is bounded by the multiplicity of the point in $D$ (again this is a local calculation and can be done in local rings).
Best Answer
Let's assume that $|kD|=|kM|+kF$ where $|M|$ is base point free and moreover $Sym ^kH^0(M)\to H^0(kM)$ is surjective for any $k>0$. This can be achieved replacing $X$ by an appropriate resolution and $k$ by a multiple. Let $f:X\to Y$ be the morphism induced by $|M|$ so that $f^*A=M$.
For [1], we wish to show that $f_* \mathcal O _X=\mathcal O _Y$. The Stein factorization $X\to Z\to Y$ is defined by ${\rm Spec} f_* \mathcal O _X$. We have $H^0(X,kM)=H^0(f_*(kM))=H^0(f_* \mathcal O _X\otimes \mathcal O _Y(kA))$ and so $|kM|$ in fact defines the morphism $X\to Y$. Since $Sym ^kH^0(M)\to H^0(kM)$ is surjective, then $|M|$ defines the same morphism.
For [2], Since $H^0(X,kM)=H^0(X,kM+rF)$, then $H^0(\mathcal O _Y(kA))\cong H^0(\mathcal O _Y(kA)\otimes f_* \mathcal O _X(rF))$. For $k\gg r$, the sheaf $\mathcal O _Y(kA)\otimes f_* \mathcal O _X(rF)$ is globally generated and so $f_* \mathcal O _X(rF)\cong \mathcal O _Y$. (See also Lemma 3.2 https://arxiv.org/pdf/1104.4981.pdf).
Hope this helps.