Measurement-Device-Independent Quantum Key Distribution (MDI-QKD) enhances security by removing vulnerabilities associated with detector side channels. Real-world implementations of measurement device independent (MDI) QKD face practical challenges such as channel asymmetry and physical imperfections, which degrade the visibility of Hong-Ou-Mandel (HOM) interference, an essential factor in determining the secure key rate. In this work, we evaluate the performance of differential phase encoded (DPE) MDI-QKD under realistic, asymmetric conditions. We analyse the effects of polarisation and pulse-width mismatches caused by channel asymmetry and identify tolerable limits for secure key generation. We introduce a plug-and-play DPE-MDI-QKD architecture that mitigates polarisation fluctuations using Faraday mirrors and also compensates for pulse-width mismatches. Furthermore, we propose an improved sifting scheme that raises the sifting efficiency from
94to
32, improving the secure key generation rates by 50% and making it especially suitable for plug-and-play systems. These results offer practical insights into enhancing the robustness and efficiency of DPE-MDI-QKD, enabling more secure quantum communication over imperfect and asymmetric quantum channels.