i too have the issue. i got my camera in september 2012 and took it into nikon service march this year. that was after spending $100 on cleaning kits. they changed the shutter. a week later i took it back again. they cleaned it. one more week and i took it in again. they cleaned it again. it's been 5 weeks or so now, about 4000 shots and the sensor looks pretty good below f16. some spots are showing up so at the end of this month, i'll get them to clean it again.
unless you can return the body, there really is no other solution. if you do return it enough times, they do start talking about giving you a new body. i'm resisting that approach as the problem seems to be going away (15K now) and the service centre is 1/2 hour from my house. also, i'm not taking pics for money. this body would be a risky purchase for a pro who isn't NPS.