just main points, anajli is going to fill out the details.
To rule out mode-matching as the reason for non-ideal output from the MZ, I suggested using the setup I have on the NW side of the PSL enclosure for the measurement. This uses two identical fiber collimators, and the distance between collimator and recombination BS is approximately the same, so the spatial modes should be pretty well matched.
The spooled fiber we found was not suitable for use as it had a wide key connector and I couldn't find any wide-key FC/PC to narrow-key FC/APC adaptors. So we decided to give the fiber going to the Y end and back (~90m estimated length) a shot. We connected the two fibers at the EY table using a fiber mating sleeve (so the fiber usually bringing the IR pickoff from EY to the PSL table was disconnected from its collimator).
In summary, we cannot explain why the contrast of the MZ is <5%. Spatial mode-overlap is definitely not to blame. Power asymmetry in the two arms of the MZ is one possible explanation, could also be unstable polarization, even though we think the entire fiber chain is PM. Anjali is investigating.
We saw today that the Thorlabs PM beam splitters (borrowed from Andrew until our AFW components arrive) do not treat the two special axes (fast and slow) of the fiber on equal footing. When we coupled light into the fast axis, we saw huge asymmetry between the two split arms of the beamsplitter (3:1 ratio in power instead of the expected 1:1 for a 50/50 BS). Looking at the patch cord with an IR viewer, we also saw light leaking through the core along it. Turns out this part is meant to be used with light coupled to the slow axis only.