Hej
Seems like you have a gear box issue, I think its related to your clutch and the pressure plate, during the long distances it will get heated and due to that it will have abnormal behavior like engine mis type vibration and/or abnormal jumps when u start from 0, 1st gear and 2nd gear .. this might with the reverse gear too.. better replaced the clutch/pressure plate otherwise it impacts your engine mounts
Cheers!