I had a similar issue.... very long story, but never fixed. Chased the problem for over 2 years from 10k service and gave up after 50k service. Probably spent close to 10 separate occasions under review, counting standard service inspections. Te dealer was good, but clearly were not supported by Nissan Australia.
As it happened...
Changed wheels at about 3000klm old to 17" aftermarket with cooper AT3 (these were to be included on the new car but were not ready when leased). Developed a fairly severe vibration, felt like a badly out of balance rear wheel. started at 80 and got worse, all gears, clutch in/out etc.... 6 wheel balances later, still could not resolve. Wheel fitter suggested driveline... Dealer started looking elsewhere, after they verified nothing wrong with wheel balance. Nissan technical rep drove the vehicle and acknowledged the problem.
It was reproduced with stock wheels/tires but, the AT3's seems to amplify it more and to an unacceptable level. However they accepted it was there with stock wheels so continued to pure the problem. Nissan Au technical also got involved and (if I believe them) the issue also went back to Japan for further support. My car was not the only one....
Prior to this I had a D40 STX 2.5 and also another 10 in the same company over the years (D40, manuals, autos, 550's) all without the problem.
The dealer acknowledged this problem ion another vehicle (550) they sold and ended up taking it back at a few thousand alms old as they could not diagnose. Nissan Aust did not support them in this, all attempt to source the problem was at their cost!.
Nissan tried fixes on mine like fixing a vibration problem with heater hoses under the dash (the Nissan tech rep said waste of time but they did it to satisfy Nissan Australia). In the end they refused to do anything until Nissan Japan gave them a fix for the is problem. On a number of cases from dealer, Nissan tech rep (ti the dealer) and the Nissan clowns on the phone reading form the file report they acknowledged a known problem on "some" D40's that they could not diagnose.
I talked about trialling options but without Nissan au agreeing to pay, the dealer would not. The dealer did tell me they tried numerous variables over a few months on another D40 550 with no success. They talked of numerous parts replaced, running with rear diff disconnected (driven through font wheels via 4WD I think they said) even loosening tray fixings and adjusting etc. with no success.
Based on my prolonged experience with Nissan, you did well to get a fix!.
I still think the issue I have would be simply fixed with something in the driveline, but they are not keen other than to advise all is in spec.
I also have a weird clunk developed over about the last 30k. A repeated clunk when cornering, first/second gear with moderate load, and inner rear wheel traction skipping) coming from the rear driveline. Say if you were going around a bumpy tight roundabout, turning from a set of lights to cross an intersection etc. Nissan are claiming suspension issue (car has an ARB 2" lift from new). ARB have inspected recently, and are sure it is driveline.....
Will see what happens as that issue is ongoing now.
I have chased on the forum here before with no luck but if anyone has any ideas I will consider anything!.......
Cheers.