That is a stroke of genius! That is actually a really good idea to use magnets to attach the cover. I may just have to steal this idea for my tonneau cover. Right now mine is just mounted with traditional hinges but it becomes a pain because I take it off all the time and for me that means having to unbolt the hinges every time. This way just mkes so much more sense. My only question is would the magnets be strong enough to hold the cover on with it partially open? Ocasionally I need to haul something without time to remove the cover so I just prop it open, and I definitely wouldn't want it to blow off while driving.
Hmmm. Oh and I know you are planning on re-purposing some hard drive magnets but if you need somewhere to get more magnets them there is a website
K&J Magnetics that sell all shapes, sizes and stregenths of neodymium magnets. I have ordered magnets from them before and as you mentioned a lot of theirs actually do come with warning lables, these types of magnets are STRONG!
But looking at your pictures it seems like trying to find a way to install the biggest possible window on the sides of an aero cap clear would be a very good idea. Honestly that's the one thing that concerns me about building an aero cap is losing visibility. Traffic where I live is usually pretty nuts. But if I had good windows on both sides and a window facing the rear I would definitely feel a lot more comfortable with one.