Just to let anyone interested know how this ended up...
I took the heater to the Seattle dealer, Sure Marine. They were great, put it on the bench right away. The diagnosis was that a grommet in the combustion air intake had been misplaced and starved the combustion air, sooting the heater and ruining the control unit. They waived the labor charge but the part was around $800! The really bad news is that Webasto denied the warranty claim because the unit was started two years and two weeks before. The heater is warrantied for 2 years or 2000 hours, whichever comes first. And the heater had only 5 hours on it, per Sure Marine!
I asked Cutwater to help and they talked with Webasto with the same result. I had hoped that Cutwater would have some leverage with Webasto, or at least take some responsibility themselves. No such luck. I believe the misplaced grommet was a latent defect, it happened before the heater was put into use, and should not have been subject to the time limit of the warranty.