Xion I had a long sleep so my thoughts are as clear as can be

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I think someone mentioned this on your bit-tech log for getting your memory and expansion slots black, a permanent black marker, it would be the safest option, it is what I would do if I wanted them black, you could even test it out on 1 of the pieces you removed where it wouldn't be seen just to see what you think, worth a try.
I think spraying a motherboard could be too risky unless you do a 100% awesome job of masking around and filling the slots so nothing gets in, I suppose you could use thin rolls of blue tack lay over the slots, I think it is doable if you really take care to cover everything except the bits that you want painting.
Oh yeah & I wouldn't worry about the mounting holes as all drives have them and they will look cool enough with them looking as if they are floating

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