I have to imagine that S&S is bound to have some options for engine modifications in-house (unless they have some sort of clause in supplying the engines to Morgan). Also, as to exhaust, there are plenty of bike shops which no doubt would gladly take your business.
Realistically, I would be focused on the other shortcomings of the Morgan build and rectifying those before adding power. Also, I refuse to do business with a company which cant bother to respond to an email/phonecall and you have S&S within "spitting distance" of where you live.