Have you gone through the ‘rough idle’ check list? (attached below).
The ‘over-running alternator pulley’, is more likely to make your belt tensioner bounce around more than it should, or make the tensioner appear to be worn.
If the rough idle is very pronounced, I would suspect something other, or in addition to a worn alternator pulley.
I have had the Dealer refer to an injector relearn on the Diesel. ECU can be set to compulsory relearn mode, via scantool.
Will do injectors, fuel pump, and EGR valve.
What angle does your ECU say the EGR valve is at, whilst on idle? What angle is it at on cold start?