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Do you think a good test would be to dremel the excess down on my current rivet? If so, how far can I go before the rivet fails?
why not make a recess on the inside of the panel so that you don't have to worry about so much bulge?
You are using what are called pop rivets. The mandrel is the steel shaft that is pulled towards the rivet gun, expanding the shaft of the softer rivet material (usually aluminum or soft steel) until it shortens and expands as far as it can, and the mandrel snaps off. There is a nub at the end that you may be able to flatten somewhat, but that is the point that attaches the two materials together, other than the rivet head. If you cut off the nub completely, you lose the holding grip.
You may have to leave the nub and make an allowance for its length by notching out the case frame.
One alternative would be something along the lines of a thread insert rive or a flush fastener, if you don't wish to drill the case. There will still be some thickness of a fastener though on the metal side. See links to see the fasteners I am thinking about:
http://www.pemnet.com/fastening_products/pdf/fdata.pdf or www.alibaba.com/showroom/flush-fasteners.html
The problem with these alternatives is that the flush side must be on the metal case side of the sandwiched plexi, and anything that holds from that side will have to have some minimum thickness. Your window, if a hair smaller, may have cleared the edges of your case and the extra wouldn't have mattered. (should have, would have, could have...but it's too late to lament that)
The more I think about it, I agree with MannyMan that you should just notch the case frame for clearance, use regular pop rivets, and touch up the paint in those areas.
...and i agree with mannyman get a fan controller for that missing 3.5 cover, or one of those sd card readers im sure you can find a while one