@Vagrant:
If this sort of thing is given as the explanation, I'll accept it. It'd be wrong biologically, but at least it means Oda would have thought about it and came up with a half-plausible concept. Any blood going into 1 part of the body has to come from other parts of the body at that same rate. Which means whole body blood pumping. Pretty much what semil said at the start of that quoted bit.
My issue isn't with partial Gear Second as a whole, although that concept itself is a bit silly. It's that at the moment we don't have the facts to understand it against the backing of what we know about how Gear Second actually functions, and my worry that we may not get an explanation.
Scientifically, you are right and partial gear 2nd is simply impossible. Regardless of whatever speeding up/slowing down/constricting blood flow method, the end result is that there is going to be huge lack of blood in other areas of Luffy's body. Looking at his frame, I estimate him around 160 lbs which would be an average of 5 litres of blood in his body. Deprived of blood carrying oxygen, Luffy's brain would cease to function in less than half a minute.
But why kill yourself over needing a logical explanation? You could also say that Gear 3 is rubbish. Imagine slapping someone with a deflated balloon. Not much damage. Blow up the balloon and tie the end. Slap someone with it. Won't hurt much would it? Force = Mass x Acceleration. The mass basically remains the same, and the acceleration actually gets slower. So in reality, gear 3 would inflict less damage than normal hitting. Why not complain about that either?
tl:dr - just enjoy the story.