First of all, what bike? Model and year, please. You posted in the Hondamatic section....do you have the semi automatic CB750?
The bottom end knock could be carbs out of sync, and most likely is, since you say someone has been working on them.
Do the 3K mile tune up and vacuum sync the carbs.
Pics of the shavings would be helpful. But start with the tune up and carb sync.