Your wife's engine - that's unfortunate it happened, but good that it's covered under warranty. (and yes, it's probably better to start your own topic for this car so other people can easily search if they've come here looking for solutions to theirs)
Hyundai/Kia have addressed body/chassis rusting issues pretty effectively from what I can tell since they first landed here years ago, and now you have a great opportunity to make the new engine last as long (or longer!) than the rest of the car.
I'd apply snake oil first on the new engine (and then drive for a while), then I'd address the PCV system (and drive for a while more) and THEN groove...all before you perform the first oil change.
My rationale:
get the goodness of the oil treatment happening as you break the engine in - protect the brand new wear surfaces, bearings and oil passages with the good stuff before the gunk builds up. THEN, because the PCV system is related to crankcase blow-by dynamics/flow/pressures, you want to treat that with the good stuff as well, and then, as all of that is setting in, you want to solidify it while the groove starts doing it's thing.
Good luck, have fun!