Thanks, the motherboard dimensions are (Dimensions • 13.68" (L) x 13.05" (W) (347.47 mm x 331.47 mm)). The 6039P appears to have space for aSuperMicro 6039P-E1CR16H 3U Flexbay Barebone Server w/ X11DPH-T 2x 1200W PWS | eBay I think that's the chassis you need, you can probably sell that X11 board for around $250, or just add another $250 for a pair of Xeon Gold 6132 CPUs and 256GB of DDR4. Either way there's still no power for GPUs, so that'll be something to figure out.
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I may have to come up with a custom case out of sheet aluminum to get the mounting holes correct. I know someone who has access to a press brake and might be able to put something together which will work. It's kludge but I don't see a workaround at this point.