Glad this worked out for you and hope the paint repair holds up. I had a similar "soap opera" with my 2010 SESG. Found a small chip on the edge of the fairing before I picked up the bike. Dealer said they'd make it right...what a clusterf--- that became. MoCo dropping the ball, then the factory closed for two weeks over X-mas, then dealer dropped the ball..service mgr handing the issue fired...had to start whole ordeal over, then the painter was backed up, painter retured the fairing with a run in the clearcoat, etc., etc. Finally, I demanded a new fairing, which the McCo agreed to. This took all the joy out of buying a new bike. I logged about 1,000 miles going back and forth from my house to the dealer to handle this issue.
Lesson learned - I WILL NEVER go through with another purchase if there are issues/repairs that are promised to take place after I pick up the bike. I should have told them to make it right first, then I'd complete the sale...my excitment about taking delivery of the bike clouded my judgement...I knew better.
Sorry for the rant, glad your bike's been made right, but I know first hand how frustrating this was for you.