What can cause vibration and noise from the chain?
If you changed the crank length then the front derailer likely needs to be adjusted, and the rear may need a few tweaks.  Also, when you change the rear cluster there can be a difference of a mm or two between old cluster and new, requiring adjustment of the rear derailer.

Have you readjusted both derailers "by the book"?

(Whether or not you used a torque wrench would have little bearing on this issue, though you need to be sure to check that your crank bolts are tight every 200km or so for the next 1000km.)