When you cut your aluminum square for the video card, just use plastic stand-offs. This does a couple of things:
1) It pretty much garantees that the aluminum will be an equal height over the pcb at all corners.
2) It raises the aluminum far enough off the pcb that it eliminates the need to cut holes for the pcb components, as well as insulating the bottom side.
3) Doesn't trap heat in the pcb because the aluminum is at least 1/2 inch from touching the PCB.
If you also put 3 or four standoffs in the center, there's almost no way you could warp your pcb by over-tightening.
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