I was playing my MC team yesterday, when the following situation came up: I MCed his Prof. X, who then MC his cyclops to blasted ajacent Storm. I then ended my action, without taking any MC click damage. My opponent said that I had to because I MCed Prof. X and Cyclops. I want to know if you have to only add the points for the initial targets of MC, or everyone who gets MC during the total action.

You only add the initial targets of the MC. Each MC is a separate action with its own set of targets. So it's not your MCer that is MCing Cyclops, it's Prof X.

So in this case, no damage to your MCer or his Prof X.

To continue the scenario...

If the mind controlled Cyclops was over 100 points (which I realize he's not, but stay with me), would the mind controlled Professor X have taken a click of damage? I know this used to be the case but I'm not sure now with the new rules.

Yes, he would have taken the click of damage in your second scenario.