What a great article and it just shows that big food controls the commodity pet food market and channels junk and crap production methods through it, just as big food does with prepackaged food for human consumption (think pink slime in McD products!).
I carried out similar research, without your level of expertise, and did come down on the side of raw food. I balanced the risks and concerns with the same care I apply to my own food — good hygiene and practice to minimise any risk. My pets have Natural Instinct (a UK brand of raw food) and love it.
My principle is to feed my pets as I do myself, try to know where the food is coming from and how it is made, have respect for the supply chain, support people who care about what they’re doing, minimize additives and sugars and the like, each naturally, eat balanced — oh and the odd rib eye and chips, glass of wine, chocolate bar etc. will not kill, just in moderation.