Can spectre use coordination in order to see past other jsa members? or no because jsa is his special TA?

I think you could, because Specter has the JSA TA...


But he's a giant, he can see over people

Exactly, he is a Giant figure so you don't need to put Coordination on him.

You can assign him the Coordination card, as he has the Quintessence symbol. As per the text of the feat, however, he will only ignore others with the Q symbol.

That said, as has been pointed out, standard figures are ignored for LoF to and from him anyway.

You can use coordination to see through other Quinstessence figure but not JSA. He can use the JSA ability and coordination says, "you can shot through figure with the same team symbol. But he a giant anyways, so you wouldn't need coordination.