I had a knock like that once. My cam chain tensioner guide had broke. This is most likely not your issue but mine sounded similar.
What is the exact year and model of your bike? Is it SOHC or DOHC?
Recently picked up a 1979 CB750K Anniversary edition. 6000 original miles hadn't been started in 10 years.
It had a big wind jammer faring on it that I took off. However, when they put it on I think they modified the electrical a little bit. (Not sure)
Well I got it all running, faring off...