Really the only know issue with the trannys are the fact that the higher gears will burn up. Im not sure if that could cause the thump. As for the second one u will need to get it aligned. The third one should be under warrenty. If not just get some 3M adhisive spray and spray the back and stick it back up. Another thing u should check on the tranny is the fluid level and the condition of it. HIH