I really empathise with you here. Buying a Morgan was, for us, such a personal thing & almost a dream come true. I think if the final product is different to your ordered spec, it must be so disappointing especially given the distance from manufacture to delivery.
The damage has now been done, though. Your wish has been tarnished & it's going to take some recompense to put things right.
From here it's all about damage limitation. Do you completely reject the car & obtain a refund, do you rectify the shortcomings and invoice Morgan or suck it up and just sort your brand new, very expensive car yourself..?
I feel for you, but as others have said, the car WILL be worth it in the end whichever way you go. It just sours the enjoyment at the moment.