Huffdaddy,
I had some cheese that floated in the whey, too (it was a Derby), and when I cut into it after ageing, it was full of tiny little holes. Tasted good, though.
Cheese contamination can happen anywhere, it wouldn't have necessarily been at the farm. There are a lot of little "thingies" floating around in the air everywhere, sometimes tough to control.
I make a lot of bread - really stuck on sourdough lately - and I do expect to have some cross-contamination from that. Haven't had too much of a problem yet.
Greg,
I've made cheddar, colby (not too successful, as it was a really weird day!), mozzerella, ricotta, and I also like Fankhauser's hard cheese recipe. I've found that Junket rennet sets up just fine when using his method to acidify the milk overnight, as long as I don't warm it to anymore than 70 degrees before adding the culture. That won't work for me in the summer, but is a good winter option.
I've only used raw milk for cheesemaking and I've only been making cheese for a year, so I can't give any comparisons. If you have specific questions, we can start a new thread so as to not hi-jack from HuffDaddy.