Lyric discussion by T_D_Phoenix 

"but if he's all you say"

would have been much better recieved had he said "but if he's even all you say"

As a validation type thing, i.e. "if jesus was even who he claimed to be"

"Would he fly from heaven into this world again?"

He's thinking that Jesus should think to not come back for what happened the first time.

He's just really confused about what happened and what Jesus thinks about it and if Jesus was even Jesus.

And no, James had nothing to do with anything at all. Glen just considers Jesus to be like a brother.

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