To further confuse matters, S&S are an excellent company with a good reputation and their engine may turn out to be better than the HD. Vibration would still concern me though. Why not ask Morgan these questions ?
I would be much much happier with the S&S iso the HD engine. (I might even want one now)
I think the X-wedge is a much better engine (bearings/cooling/crackshaft etc) and gets good reviews; This is e.g. what Alan Cathcart

said in Motor cyclist; "Despite lacking a counterbalancer, the 95-horsepower X-Wedge motor is satisfactorily smooth all the way across the rev range. It's very refined in terms of operation, too, starting, idling and injecting without any issues to speak of."
Opening up the V-angle, the one piece crankshaft and changing to journal bearings is probably much better than having counter balancers in a 45 degree HD big twin. And I guess there will be a much heavier fly-wheel and clutch assembly (mazda?) in the 3-wlr compared to a motorbike, also reduces vibration. Plus, the counterbalanced HD engines also vibrates at cruising speed, they are stil pretty agricultural machines. With any big twin, expect to have to tighten some bolts now and then. But the big twin rumble & vibes will be part of the magic of driving the 3 wlr as it is with big twin motorcycles.
If you still want a HD engined 3-wlr, look at this;
cyclecar Apparantly been made in the US for the last 15 yrs or so under Morgan license. It has the Evo-B motor (balanced), weighs 950lbs, does 120mph, costs 48k US.
Cheers, JJW