You get an MSO for the Jims engine and not your original S/N on it. This is not a street legal motor, nor is it a HD motor. It's an aftermarket engine that HD licenses Jims to build using their current design platform, and is only available thru HD dealers. No other aftermarket crate engines are available for these bikes. Theoretically you'd have to get the bike re-VIN'd if you really wanted it legit. But taping a copy of the MSO to the bottom of your seat and always having it with you should be good enough. But it might effect resale of the bike someday, since you have no engine tied to the VIN anymore. In Ken's case, he was only getting a rebuilt engine from HD. So he's taking all the costs associated with the new parts he needs, and all the labor, and putting that toward the Jims. He will not wind up with a new 110 engine with his S/N. He'll have his original POS broken 110 to take up space in his garage. But I wouldn't get rid of them cases with his S/N on it tied to his VIN. 
Hoist! 
Howie, I see a different scenario:
I have a bad motor that the MOCO will replace and pay the labor. MOCO sends a new 110" motor with VIN, and pays dealer labor to have it installed, gaskets, o rings etc.
I then buy a Jims motor from the dealer. He installs the Jim's at no cost, follow? I then take home a new 110" engine and the bike with the Jim's.
My cost then is the cost of the engine, but I have a new motor with VIN in the garage.
Why would it not work that way?
Everyone is happy, almost. Now you could swap it back before selling and its a new matching motor!