I'm Translating YES 《close to the edge&#122

I think the "Two million" refers to the majority of people in the world who are unhappy, compared to the "two hundred" who are now followers (the "Interest could be laid upon the children of her Domain/followers of her son" line). 

Then the last stanza, Jon speaks of himself: In charge of who is there in charge of me" is jigsaw grammar, but together with "Do I look on blindly and say I see the way?", it seems to refers to his confusion and uncertainty "who's in charge of me". The last lines say the truth is right in the scriptures, but when will I reach enlightenment and see you for myself? I'm assuming the valley/the man with his arm is that person. Or whatever figure Jon thinks up. And then the song's music seems to reach a high state too, so I think that's the intended message. 

This has some direct Jon quotes too: http://genius.com/Yes-close-to-the-edge-lyrics/

“The song came about because Steve was playing these chords one day, and I started singing, ‘Two million people barely satisfy.’ It’s about the incredible imbalance of the human experience on the planet.” – Jon Anderson

“There are several lines that relate to the church. Churchgoers are always fighting about who’s better and who’s richer and who’s more hip. So at the end of the midsection there’s a majestic church organ. We destroy the church organ through the Moog. This leads to another organ solo rejoicing in the fact that you can turn your back on churches and find it within yourself to be your own church.”