Uh, I don't know what to say for the counters. The window is so small that I only really see any use for it when your opponent is being REALLY predictable with strings.
I don't know if you have already have VF4:Evolution or not, but the tutorials in that are FANTASTIC and most of the basics still apply to VF5. I believe counter scenarios are covered pretty well under some of the more counter-heavy characters (Aoi, Akira). I recommend picking it up for that feature alone.