1) The 2 on 1 was a non issue. Good example of announcers worshiping Lance and tearing down Contador at every chance. Now if the goal was to win the stage then the 2 have a huge advantage over the one. Several things they can do. One attacks and then Cantador either has to work to catch him or lose the stage. If he counters (and in so doing uses as much energy as the original attacker) then the one that did not attack stays on Contadors wheel and the attacker sites up and catches on the back. Reverse positions and repeat (or same attackes 2 times in a row, mix it up just enough Contador does not know who is going next). Problem is on a climb Contador has a burst second to none, so attack and he catches you, perhaps sits on yuor wheel for a second or two and then passes.
If Contador were a poor decender he could have been in trouble, we saw he is at least as good as the Schleks.
2) You nailed it. No time gap. Contador seems ot have been being careful at the finish. Note the stage went to Frank, not Andy. Contenders often let a non-contender have a stage if they have worked. It is very acceptable not to, what makes you enemies is to have a misunderstanding.
3) Drafting does make a difference in the mountians. Not for me, and likely not for you. Remember the drag goes up as the square of the speed. Those guys are going about 3 times as fast as I can (on long uphills, I, less of a joke on the flat, might even be able to hold a freindly wheel on a training ride). That comes out to almost 10 times the wind drag. But on the next to last stage it was entirely different. Huge wind once they were out of the trees. That kicked it from minor advantage to huge advantage (depending on the wind direction vrs. the road at any given point). Actually wind in hte mountian is pretty common. It can end up huge.