This is not the unitary that you have to implement: you need a two-qubit unitary
$$
\frac{1}{\sqrt{3}}\left(\begin{array}{cccc}
1 & 1 & 1 & 0 \\
1 & \omega & \omega^2 & 0 \\
1 & \omega^2 & \omega & 0 \\
0 & 0 & 0 & \sqrt{3}
\end{array}\right),
$$
where $\omega=e^{2i\pi/3}$, the point being that if you introduce an ancilla qubit in the state 0, apply this unitary, and then measure in the computational basis, the 3 measurement outcomes 00, 01 and 10 correspond to the 3 POVM elements.
I don't (yet) have a circuit implementation for this. You'll see the paper you cite carefully avoids talking about the Fourier transform in non-power of 2 dimensions. You certainly could use the standard constructions based on Givens rotations, but the result is going to be fairly horrible.
Here's an attempt at a circuit. I've made a few tweaks since I last ran it through a computer to check, so it's always possible that a slight error has crept in, but broadly...
Here, I'm using $Z^r$ to denote
$$
\left(\begin{array}{cc} 1 & 0 \\ 0 & e^{i\pi r} \end{array}\right),
$$
and
$$
V=\frac{1}{\sqrt{3}}\left(\begin{array}{cc}
1 & \sqrt{2} \\ -\sqrt{2} & 1
\end{array}\right).
$$