Honestly, the story is not that hard to get. Just concentrate more or some such thing.
Anyways, there are lot of stuff in Lain to analyse, but I find it irrelevant since Lain is about portraying this certain set of feelings.
Like you know, when you're reading the Howl or some other poem that is full of reference, you tend to pay more attention with understanding the references than what the poem is really trying to say. I mean, the references do underline the message but they are not the message itself.