No it will not if you have a bad clutch it would cuase hard shifting and possible engine kill. if your transmission is skipping 2nd gear you are looking at a bent shift fork in the transmision, I have come across this before and it is not fun to get to, to replace. the engine knock on the other hand can you tell where its coming from... top front of engine, lower front, rear. does the knock sound like a thud, tap, chain rattle. fast/slow at idle? I would need clarification on the knock