Sorry to hear of the engine problems so early in your ownership of the new to you bike. Lifter failure up until 14 and up was and has been very common. They (HD) uses a new style now that is proving only slightly better for some.
A lot of people I know change out the lifters BEFORE or very shortly after they ride the bike.
Unfortunately for you, when a lifter fails, the debri contaminates the entire motor. Everything inside the cases gets the super fine grit thru-out. The crank, its bearings, cam and its bearings, camplate and oil pump, pushrods and rocker arms, valve seals and possibly guides. Over here it is common for HD to send a replacement engine. I assume their policy is different there.
It does sound like your dealer is building a new engine from ordered parts. Don't let tem use anything that was in the original motor. Talk to your dealer about using S&S Standard lifters instead of their latest, greatest.
Also make sure that the oil tank and its lines are thoroughly cleaned and as new, the tank and lines will be full of bad stuff you don't want back in the engine.
A fellow in the US just reported a lifter failure at 18 miles on a new 16 CVO. Another went 7500 miles, then boom, replacement required and done. Nuff said. fwiw twin otter