Sorry to hear your problem and this would make a good topic in Technical about PCM/ECU's. (Power train module/electronic control module)
Yes something seems wrong with the dealer, however my experience of vehicle manufactures and these type of units is to get the dealer to confirm it has failed and then find a company who repairs them as it is a lot cheaper! Up to 85% cheaper! I do not have experience of the E450 units but I see there are plenty of places who advertise on the internet. Companies normally not only repair the part failed on the module but also components they know will fail soon. You may well find the unit is not manufactured by ford as companies a lot of vehicles use the same units and when removed you can look up on the internet the type and see common problems. Normally it is best to get your own unit repaired and not buy another one.
Check your manual as I think the E450 after having the battery disconnected (for module unplugging)has to teach itself again and there is a procedure when you start the engine and the first few miles. This is common with other units.