Ah, that's a good point. Though, if it only affects newborns, we'd then need to predict how the US would be in 25 years, before any changes happen. The virus could have been an anti-Zika virus, that spread to most of the population, but only really had an effect on those who were either in sexual maturity, or reaching it, but not those that have began to "decline".

Magic tag might be new, dunno. A "beneficial virus" could be created for any number of reasons. Maybe to control the spread of cancer, or to fight a specific bacterial infection. Maybe it was just an experiment on mice that the scientists contracted, and spread to the population. Whatever the cause, it won't be a few years (maybe even a decade or two) until they even notice it happening. By then, they won't be able to link it to the actual cause. In fact, that's probably something to consider for an answer; nothing will noticeably change for at least a several years.

Viruses are microscopic, and often contagious entities that can spread far enough to force a mutation. Assuming someone created a non-lethal virus that gave every human in the US the required genes, without the consent of the population, then it's entirely possible for this sort of scenario to occur. Of course, there's always just "magic" (as tagged in the question)

There are two solutions to this. First would be that the portals must share a vector in space. Thus having portals facing each other is not possible. The proposed scenario would instead have mass M fall into the Portal A, and fly up out of Portal B. Second is that you're not actually creating a perpetual motion machine. It only appears like it, because of the frame of reference. After all, the "machine" gains its energy from the Earth, and with each pass, the Earth's mass would also be effected. Moving a pebble into near light speed is less energy than moving Earth a few inches.

It's not too far-fetched to assume this sort of scenario happened. The transistor and micro-chip being invented before a solid grasp on genetics and biology is formed isn't too far fetched. The thing is, when you have the technology to create something like a microchip, it becomes increasingly difficult to not notice that cells exist. In fact, I'm pretty sure vaccinations, one of the things you mention this society knows about, should require some basic awareness of cellular life, though I could be wrong.