Harley has a very loyal following here in the states, to the point some of the more 'die hard' enthusiasts would scorn at the notion of using the HD brand to market for a non US moniker. With S&S being made in the USA and over all a more neutral brand, it still brings the same respect and (better) performance than HD. Also, HD has a reputation to uphold, as most all the Harley riders I know would consider themselves leather-clad road-warriors. And, while S&S may provide the upgrades to these bikes my hog-riding friends have, the S&S brand is more in tune with customs and show bikes and it really is a more applicable brand to pair with Morgan.
As for any engineering frets, it is something that comes with being an 'early adapter' to any product. I am sure, there are bound to be some aspects that can be improved upon. I was an early adapter on the E90 and the R56 and while they have both had some faults, they have both turned out to be very enjoyable. And, with Morgan being a company that is in its centennial I feel it must have a good grasp on this, so I am not worrying about it.