First, I'll prove a formula that I always like to keep in hand. What is the $d$-dimensional Fourier transform of a rotationally-symmetric function $f(x)$? That is,
$$
\tilde{f}(p) = \int d^d x \, e^{i \mathbf{p} \cdot \mathbf{x}} f(x).
$$
Here, the magnitudes are $x = |\mathbf{x}|$, $p = |\mathbf{p}|$. I'm going to work with the Euclidean norm, $\mathbf{p} \cdot \mathbf{x} = p_1 x_1 + p_2 x_2 + \cdots + p_d x_d$, and we'll analytiically continue later.
We can set this up in hyperspherical coordinates. Further details can be found on Wikipedia. The coordinates are
$$
\begin{align}
x_1 &= x \cos \varphi_1 \\
x_2 &= x \sin \varphi_1 \cos \varphi_2 \\
x_3 &= x \sin \varphi_1 \sin \varphi_2 \cos \varphi_3 \\
& \vdots \\
x_{d-1} &= \sin \varphi_1 \cdots \sin \varphi_{d-2} \cos \varphi_{d-1} \\
x_{d} &= \sin \varphi_1 \cdots \sin \varphi_{d-1} \sin \varphi_{d-1}
\end{align}
$$
Here, $\varphi_{1}$, $\varphi_{2}$, ..., $\varphi_{d-2}$ range over $[0,\pi]$, and $\varphi_{d-1} \in [0,2 \pi)$. The spherical volume element in these coordinates is
$$
d^d x = x^{d-1} \sin^{d-2} \varphi_1 \sin^{d-3} \varphi_2 \cdots \sin \varphi_{d-2} \, dx \, d\varphi_1 \, \cdots \, d\varphi_{d-1}.
$$
We choose our coordinates so that the $x_1$ coordinate is in the same direction as $\mathbf{p}$, that is, $\mathbf{p} = (p,0,\cdots,0)$. So the integral is
$$
\tilde{f}(p) = \int d^d x \, e^{i x p \cos \varphi_1} f(x).
$$
We first perform the $\varphi_1$ integral. After some transformations, we recognize an integral representation of a Bessel function (equation 10.9.4 on the link):
$$
\int_0^{\pi} d \varphi_1 \, e^{i p x \cos \varphi_1} \sin^{d-2} \varphi_1 = 2 \int_0^1 dz \, \cos(xpz) (1 - z^2)^{(d-3)/2} = \frac{ \pi^{1/2} \Gamma\left( \frac{d-1}{2} \right)}{\left(\frac{1}{2}xp\right)^{(d-2)/2}} J_{\frac{d-2}{2}}(xp).
$$
The rest of the integral is the surface area of the $(n-2)$-sphere, which is the familiar expression $2\pi^{(d-1)/2}/\Gamma[(d-1)/2]$. So,
$$
\tilde{f}(p) = \frac{(2 \pi)^{d/2}}{p^{(d-2)/2}} \int_0^{\infty} dx \, x^{d/2} \, J_{\frac{d-2}{2}}(xp) f(x).
$$
This is a bit of a digression, but if you work with dimensional regularization a lot (or you like to work in arbitrary dimensions), this is a very useful formula to have around.
With this, the rest of your calculation becomes very straight-forward. You have $f(x) = 1/x^4$, so the integral becomes
$$
\tilde{f}(p) = \frac{(2 \pi)^{d/2}}{p^{d - 4}} \int_0^{\infty} dx \, x^{d/2-4} J_{\frac{d-2}{2}}(x).
$$
This is another point where one looks up properties of special functions (eq 10.22.43 in the link). We see that the integral only converges when $4<d<9$, but in this range of $d$, we have
$$
\tilde{f}(p) = \frac{2^{d-4} \pi^{d/2}}{p^{d-4}} \Gamma\left( \frac{d-4}{2} \right).
$$
If we expand this near $d=4$, we get
$$
\tilde{f}(p) = -\frac{2 \pi^2}{4 - d} + C - \pi^2 \log(p^2),
$$
where $C \approx 19.28$ is a constant. One can Wick rotate back to your preferred metric.
The addition of an $i \epsilon$ on one side of your equation but not the other involves the addition of some physical (e.g. "Feynman") prescription for your problem.