Here is yet another solution, which probably is not a physicist's way of thinking.
After Wick rotation, we may work on Euclidean space. The function $f(k_E) = |k_E|^{-4}$ is not square-integrable on $\mathbb{R}^4$, however, so its Fourier transform does not exist in ordinary sense. A moment of thought suggests that it can be realized as distribution on the space
$$ \mathcal{A} := \{ \varphi \in \mathcal{S}(\mathbb{R}^4) : \textstyle \int_{\mathbb{R}^4} \varphi(\epsilon) \, \mathrm{d}^4\epsilon = 0 \}, $$
where $\mathcal{S}(\mathbb{R}^4)$ is the Schwarz space. Then computing
$$I(\epsilon) = i \check{f}(\epsilon) = \frac{i}{(2\pi)^4} \int_{\mathbb{R}^4} |k_E|^{-4} e^{i\epsilon \cdot k_E} \, \mathrm{d}^4 k_E$$
in distribution sense amounts to identifying the following pairing
$$ \langle I, \varphi \rangle = \langle \check{f}, \varphi \rangle = \langle f, \check{\varphi} \rangle, \qquad \forall \varphi \in \mathcal{A}. $$
Since $\check{\varphi}(0) = 0$ and $\check{\varphi}$ has rapid decay near infinity, the pairing $\langle f, \check{\varphi} \rangle$ is realized as Lebesgue integral. Then by the Fubini's theorem,
\begin{align*}
\langle f, \check{\varphi} \rangle
&= i \int_{\mathbb{R}^4} \frac{1}{|k_E|^4} \check{\varphi}(k_E) \, \mathrm{d}^4 k_E
= i \int_{\mathbb{R}^4} \bigg( \int_{0}^{\infty} t \mathrm{e}^{-|k_E|^2 t} \, \mathrm{d}t \bigg) \check{\varphi}(k_E) \, \mathrm{d}^4 k_E, \\
&= i \int_{0}^{\infty} t \bigg( \int_{\mathbb{R}^4} \mathrm{e}^{-t |k_E|^2} \check{\varphi}(k_E) \, \mathrm{d}^4 k_E \bigg) \mathrm{d}t.
\end{align*}
Using $\langle \mathrm{e}^{-t|\cdot|^2}, \check{\varphi} \rangle = \langle (\mathrm{e}^{-t|\cdot|^2})^{\vee}, \varphi \rangle$ and the formula $\int_{\mathbb{R}} \mathrm{e}^{-tx^2}\mathrm{e}^{ix\epsilon} \, dx = \sqrt{\frac{\pi}{t}} \mathrm{e}^{-\epsilon^2/4t}$ for $t > 0$, we have
\begin{align*}
\langle f, \check{\varphi} \rangle
&= i \int_{0}^{\infty} t \bigg( \int_{\mathbb{R}^4} \frac{1}{(4\pi t)^2} \mathrm{e}^{-\frac{|\epsilon|^2}{4t}} \varphi(\epsilon) \, \mathrm{d}^4 \epsilon \bigg) \mathrm{d}t \\
&= \frac{i}{(4\pi)^2} \int_{0}^{\infty} \frac{1}{t} \bigg( \int_{\mathbb{R}^4} \mathrm{e}^{-\frac{|\epsilon|^2}{4t}} \varphi(\epsilon) \, \mathrm{d}^4 \epsilon \bigg) \mathrm{d}t.
\end{align*}
We want to finalize the computation by switching the order of integration, but the Fubini's theorem is not applicable in this case and even the heuristic computation produces a divergent integral. Thankfully, using the fact that $\int_{\mathbb{R}} \varphi(\epsilon) \, \mathrm{d}^4\epsilon = 0$, we can regularize the inner integral so that the Fubini's theorem works:
\begin{align*}
\langle f, \check{\varphi} \rangle
&= \frac{i}{(4\pi)^2} \int_{0}^{\infty} \frac{1}{t} \bigg( \int_{\mathbb{R}^4} \big( \mathrm{e}^{-\frac{|\epsilon|^2}{4t}} - \mathbf{1}_{ \{ t \geq 1 \} } \big) \varphi(\epsilon) \, \mathrm{d}^4 \epsilon \bigg) \mathrm{d}t \\
&= \frac{i}{(4\pi)^2} \int_{\mathbb{R}^4} \bigg( \int_{0}^{\infty} \frac{1}{t}\big( \mathrm{e}^{-\frac{|\epsilon|^2}{4t}} - \mathbf{1}_{ \{ t \geq 1 \} } \big) \, \mathrm{d}t \bigg) \varphi(\epsilon) \, \mathrm{d}^4 \epsilon.
\end{align*}
Now the inner integral can be computed using the substitution $u = |\epsilon|^2/4t$ as follows
\begin{align*}
\int_{0}^{\infty} \frac{1}{t}\big( \mathrm{e}^{-\frac{|\epsilon|^2}{4t}} - \mathbf{1}_{ \{ t \geq 1 \} } \big) \, \mathrm{d}t
&= \int_{0}^{\infty} \frac{1}{u} \big( \mathrm{e}^{-u} - \mathbf{1}_{ \{ u \leq |\epsilon|^2/4 \} } \big) \, \mathrm{d}u
= \log\frac{4}{|\epsilon|^2} -\gamma.
\end{align*}
Here, $\gamma$ is the Euler-Mascheroni constant. Therefore it follows that
$$ I(\epsilon)
= \frac{i}{(4\pi)^2} \bigg( \log\frac{4}{|\epsilon|^2} -\gamma \bigg)
= \frac{i}{(4\pi)^2} \log\frac{1}{\epsilon^2}. $$
The last equality follows from the fact that constants as distribution on $\mathcal{A}$ is equal to zero, i.e., for any constant $c$ we have $\langle c, \varphi \rangle = 0$ for all $\varphi \in \mathcal{A}$.