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don't worry about it. one thing you might consider is that you probably have enough room vertically to have the motherboard on it's side, rather than laying flat as you have it. At least experiment with different angles. I'm fairly certain this is still possible if you're looking for something that just drops right in like that. The other thing you can do, if you've got some soldering skill is make your own VGA cable. Use individual strands of CAT5 type wire to make the connections, get a fresh VGA D-Sub connector pair (like you are making an extension cable) and get to soldering. You will be smart enough to secure the wires with zip ties when you are done, that way you don't need a big molding or strain relief to soak up all that space in the back. You could manage USB and power the same way.
Not sure if that all came out clearly but i've got a pretty good reference to go from if you need me to help out. good luck!
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