Sinister Mastermind: Adjacent friendly characters possessing the Sinister Syndicate team ability can’t have their Speed or Attack powers countered.

Four Arms and Four Eyes: Doctor Octopus can use Perplex four times during your turn, but only to modify his own combat values.

Tentacle Flurry: Doctor Octopus can use Flurry.

Can a wildcard using the Sinister Syndicate team ability be protected by Sinster Mastermind?
Only if the wildcard actually possess the Sinister Syndicate team ability as well as the wildcard team ability (currently,WS #055 Sandman is the only such character). Wildcards do not possess other team abilities, they only use them.

Because of the Rule of Three, Doctor Octopus could only use his Perplex on any one combat value three times, correct? He would have to use the fourth Perplex on another combat value, right?
No. A combat value can actually be modified as many times as there are modifiers available on the map. Once, twice, ten times... even 100 times if you can somehow swing it. All the Rule of Three does is then say, when the combat value is actually used, "What is the total modification on this combat value? If it is greater than +/- 3, we'll cap it at +/- 3."

This can be especially useful when you know a negative modifier is coming your way. For example, the HYDRA team ability applies a -1 modifier to the defense values of characters attacked with ranged combat attacks under the proper conditions. If Doctor Octopus was facing some HYDRA characters, he might want to modify his defense value with all four Perplexes so that he'll have some extra insurance if the HYDRA modifier kicks in. A total modification of 4 - 1 = +3 modifier to defense value is going to be more useful to Doctor Octopus than a total modification of 3 - 1 = +2 modifer.