As soon as the mage wakes up, he automagically declares himself as Counterspelling for himself. The only way a Mage doesn't get to Counterspell is if you catch them so blindsided they don't even get a chance to go "Hu-wha?!" before you smack them upside the head with that Stunbolt.
As for Question 2, you're forgetting about being able to set the Force of the spell, which is the part that caps hits. I'm assuming that you're assuming Force = Magic, since that's how the math works out.
There are a couple other errors as well.
#1: Hits are capped by Force before the resistance check, so Bob The Mage is slinging 5 hits at Fred The Ganger. Period. End of line. The 6th hit is utterly wasted.
#2: The target's actual Willpower rating has nothing to do with the amount of hits he resists, except as part of the DP for his resistance roll. In your hypothetical scenario, Fred resists 2 hits leaving Bob with 3 net hits and dealing 8S, not 6S.
Casting Hits (CH) = Rolled Hits or Force, whichever is less
Resist Hits (RH) = Hits on Willpower (+ Counterspelling, if any)
CH - RH = Net Hits