Just removing the 3.5inch spinner from up there will improve circulation. While you can supposedly move that 3.5-inch tray/drive to the bottom ... I would just put that spinner in an external USB-3 enclosure or a different machine. Get you a Samsung 1tb 860 or 870 2.5inch SATA-SSD for new Drive-D, and stick that down in the bottom tray instead.
So I ordered my PC with a 1TB hard drive and a 500GB NVMe SSD BOOT drive. I wanted to add another intake fan in place of where the 1TB drive is. If I do this...remove the hard drive...will everything else work fine? It should be as simple as just removing and hard drive and never looking back correct?  512GB M.2 PCIe NVMe SSD (Boot) + 1TB 7200RPM SATA 6Gb/s (Storage)
Aurora R10, removing front HDD to add intake fan questions