More progress yaaay.
I'm getting close.
I decided to use proper subrack hardware to support the board. I will have to cut the rails, but I can live with that.
Cost estimate so far:
-Sheet metal top, bottom, front bezel and rear cover from SendCutSend ~$130
(including bending, countersinking and threading the top and bottom and anodizing the front)
(it would be much cheaper with quantity, and structurally neither the front nor the rear panel is needed, but it looks nice and won't short)
-Subrack hw - 1pc 19" horizontal rail with threaded insert, 10pc card guides ~$20
-PCB ~120x60mm 6 layer, JLBCB more expensive stackup to meet the trace impedance 10pcs. ~$140
-Press fit connectors - MiniSAS, CompactPCI 4pcs - $75
-Other PCB parts + screws ~$15
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$380 for the prototype (with PCBs to spare)
I was planning to put fan(s) in the cage. A 70x70x10mm would fit fine. I decided to ditch that though, as the PC case this would go into needs modification anyway to allow airflow through the drive bay and if I have to do that then fitting a much larger fan (120mm) is not a lot more hassle, promising better cooling.
Thanks for the PCIe diagnostics tip. I'm not too much of a linux person, but I can get a live image running or something I guess to check if I can't find a good Windows alternative.