One of the main draw backs of the measurement was the polarisation was not aligned properly in the setup. So, then the next step was to identify the polarisation at different locations in the beam path and to maximise the polarisation to either S or P component.

So, we introduced HWP at the input beam path after isolator as shown in attachment #1. Also, the polarisation was tested at positions P1, P2, P3, and P4 shown in attachment #1 by placing a polarisation beam splitter at these locations and then by observing the transmitted (P component) and reflected light (S component) using power meter.

The observations at different locations are as the follows

These observations show that the P and S components are almost equal, and this is not a good polarisation arrangement. At this point, we also had to check whether the incoming beam is linearly polarised or not.

To test the same, the PBS was placed at position P1 and the P and S components were observed with power meter as the HWP is rotated.Attachment # 2 shows the results of the same, that is the variation in P and S component as the HWP is rotated.

This result clearly shows that the input beam is linearly polarised. The HWP was then adjusted such that the P component is maximum and coupled to the MZI. With this orientation of HWP, the polarisation observed at different positions P1, P2, P3, and P4 are as follows.

This shows that the polarisation is linearly polarised as well as it is oriented along the P direction (parallel to the optical table).

We have the polarisation maintaining fiber (PM 980) as the delay fiber. The polarisation of the light as it propagates through a PM fiber depends on how well the input beam is coupled to the axis (slow or fast) of the fiber. So, the next task was to couple the light to one of the axes of the fiber.

The alignment key on the fiber is a good indication of the axis of the fiber. In our case, the alignment key lines up with the slow axis of the fiber. We decided to couple the light to the fast axis of the fiber. Since the incoming beam is P polarised, the output fiber coupler was  aligned such that the fast axis is parallel to optical table as possible.

A PBS was then introduced after the fiber output collimator . There is a HWP (marked as HWP2 in attachment 1) in front of the input coupler of the fiber as well. This HWP was then rotated and observed the P and S component from the PBS that is now placed after the output coupler with a power meter.The idea was , when the light is coupled to the fast axis of the fiber, we will see the maximum at the P componet at the output

Attachment # 3 shows the observation. 

In this way I tried to find the orientation of the HWP2 such that the P component is maximum at the output. But I was not succeeded in this method and observed that the output was fluctuating when the fiber was disturbed. One  doubt we had was whether the fiber is PM or not . Thus we checked the fiber end with fiber microscope and confirmed that it is PM fiber. 

Thus, we modifed the setup as shown in attachement # 4.The photodetector (PDA55) was monitoring the S component and the output of the detector was observed on an oscilloscope. We rotated the HWP2 such that the S component is almost minimum. At the same time, we were disturbing the fiber and was observing whether the output is fluctuating. The HWP2 angle was tweaked around the minimum of S component and observed the output with disturbing the fiber. This way we found the orientation of HWP2  such that the light is coupled to the fast axis of the fiber and the output was not fluctuating while we disturb the fiber. We tested it  by heating the fiber with a heat gun as well and confirmed that the output is not fluctuating and thus the light is coupled to the fast axis of the fiber.