To the first question, concentrating all the pigs would potentially breed more virulent pig diseases. The crossover events stem more contact between humans and pigs. I’d think traditional farming would be more likely to encourage a viral cross-over. The big crime of the factory farms is the indiscriminate use of antibiotics, breeding antibiotic-resistant strains of bacteria – a serious problem in it’s own right.

As far as comets spreading viral materials – I seriously doubt it.

Any thoughts as to whether, when the tails of some comets intersected earth’s path, they left behind the biological materials that are the source of [some] viruses and, therefore, are the origins of [some] viruses independent of mainstream evolution?

Giant commercial pig farms just tend to concentrate what has already been the case for centuries – the link between people, birds and pigs in the spread of influenza. Wild, migrating birds spread the latest virus over major areas. Some of the viruses leap over into a population of livestock, like pigs. Then some of the viruses leap over to a population of farmers, who then spread it around to the rest of us.

Check out the genetic lineage of the current flu.