Thank you for recommending Osama.
I took my car to him today. I told him the entire issue and also showed him your comment about Speed NT Sensor readings.
After spending 2 Hours checking, scanning and driving the Car, he was also not able to determine the cause.
He said that Speed NT Readings are fine. His initial assessment is that the issue is neither of Gearbox or Kit.
He said that he thinks it might be compatibility issue or some electrical wiring Glitch that is causing the problem.
He said to bring the Car to him tomorrow morning again at 9am and he will thoroughly check it and will let me know by evening if he can diagnose the cause of this issue.