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I can point you in the right direction but I shouldn't spend a ton of time on this. Long slow crappy weather weekend is making this very doable right now but long term I need to focus elsewhere.
Please checkout my updates - while the devil is in the details this doesn't seem that tricky.
Android connect to the wacom sensor and you use libgtk-framebuffer to do a higher level drive on the framebuffer (draw the menus). Annotation turns on and uses the x,y output to do the drawing (IMO should do pressure as well if possible) The chip does transparent overlay so it drives the annotation layover.
The nook uses the same EInk display and the downgraded driver chip(3521) (and android)
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