Since you are having trouble shifting into gear but it gets better after a few minutes of idling I'm wondering if the primary/drive clutch is partially engaging? Is the engine idling faster at first but idles slower after a few minutes? When you start it and it's still in neutral take a look a the drive belt to see if it's moving.
Are you getting the knocking sound only when in gear? Does it knock when you are in gear but not moving or only when you are driving?