Here's how I take it for what it's worth.
Q1. I read somewhere the song is mostly about Young's childhood memories. He had his formative years in a town called Omemee in northern Ontario, and it was not all happy memories, primarily because of his parents' divorce. So I would guess he's mostly singing about the period of helplessness he went through as a young boy.
Q2. "with dream comfort memory to spare". I would interpret it as "abundant comforting memories worthy of dreams", or something like "dream-like comfortable memory to spare". This is in reference to the town he grew up in, which was supposedly a peaceful small town, so it probably means the happy, comfortable side of that part of his life.
Q3. "Blue blue windows behind the stars". It sounds to me like young Neil yearning for an over-the-rainbow place he can escape to. He says in verse one "And in my mind, I still need a place to go", which seems to suggest he had a lot of unsettling experiences in those days.
About a year before Helpless, Neil Young released Cowgirl in the Sand (my favorite) which seems to describe similar (though more cryptic) sentiments. Cowgirl is probably looking back at his life at that point, with lots of success under his belt, but it seems like he's still as helpless as he is happy.
(3rd verse of Cowgirl in The Sand)
Hello woman of my dream....With dream comfort memory to spare,
Is this not................................And in my mind
the way it seems....................I still need a place to go
Purple words..........................Blue, blue windows
on a grey background............behind the stars
...
Anyway, classic rock was a lot of fun :-)