Unfortunately yes, you're not the first one and probably not the last.
Anyway it looks like you got most of the points, so I would expect anybody who would bother to read a thriller story is the first place would be attentive enough to be able to get them. [White Box]... Yes it's meant to remain a mystery at this point in the story and only serve as one extra reminder that this is somehow connected to Accelerator. I'm surprise you didn't find Alice, the crazy one, cute with her banter with her usagi-kun, personally I thought I didn't give her enough crazy scenes.
Oh yeah, you forgot the [Dormouse Numbers], that one is important too... By the way, I don't suppose the Alice in Wonderland referrences stood out much for you?