JV's - Very first out of the Fujigen factory. Fender Japan's first guitars. Various "trim levels" of 50's and 60's replicas mainly, but there were some other models.
SQ's - This run started a little later, primarily with 70's inspired guitars. Ran along side JV's in assembly until late 1984. Slightly lesser quality components overall than most JV's. First to be exported to the U.S. for sale (JV's were only exported to Europe as Squier or were Fender domestic models).
E series and A, B, C series. Started as the JV and SQ lines ended production. Maybe slightly less quality components than SQ as a whole.
Keep in mind -- what I've written above is a gross oversimplification. There were a variety of models, "trim levels" and other factors throughout each of those serial runs.
The earliest JV's are considered of the highest quality, on par (some argue even better than) their US counterparts of the day. Some were equipped with some US components (intentionally and unintentionally).
I'd recommend doing some serious research to be sure of what you want. Two great places to start are the Japanese Vintage forums at Squier Talk (obviously, you've already found that one) and 21frets.com. Spend some time there. You'll learn a lot.
That said, I'd be happy to own almost any Fujigen made Squier or Fender guitars.