If Ms. Marvel chooses the first option of and modify combat values +1, does the entire trait gain Protected: Pulse Wave? Would she be able to use Shape Change while during Pulse Wave?

The Giant symbol grants the Great Size keyphrase. That keyphrase has Protected: Pulswave so Great Size still works during pulsewave but it does not have PROTECTED: Pulsewave which is what would prevent pulsewave from even targeting the figure.

This has nothing to do with “Protected” vs. “PROTECTED”.

“Protected: Pulse Wave” protects the power or ability that it is part of, so it can be used during a Pulse Wave attack.

In this case, Ms. Marvel’s trait grants the combat symbol . Having that symbol then grants Ms. Marvel the Keyphrase Ability “Great Size”, which includes “Protected: Pulse Wave”. I don’t believe anything beyond that Keyphrase Ability is protected, though.

If the trait itself granted “Great Size”, then it would probably inherit “Protected: Pulse Wave”, just like STOP powers do, but that’s not the case here.