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Case specifications are published as best cases: the longest card with no front radiator fitted, the tallest cooler measured at the deepest point of the side panel. Real builds combine those conditions, and the combination is where an assembly stalls late at night with the panel refusing to close.
Work in the order the parts stack. Board width first, because it sets the tray and the cable channel behind it. Then cooling, because radiators consume the clearance everything else needs. Then the card, then the drives, then the cables. Whatever room is left over is convenience rather than capability.