I'll say it again:
Replace The Backplane with Wires
As in 1 (one) SPI channel PER HASHBOARD going direct to a controller. I hope to god you didn't have all the hashboards sharing a common bus on the backplane before - because I can't imagine trying to get that to work.
Dear Jonny,
The PCIE connector has 98 pins and there are 5 connectors in each case.
If you still believe that this can be done even on one X3 (not to talk about mass production) you are welcome to come to our office and try to do this yourself.
Regards!
Surely most of those 96 pins are power and the backplane doesn't have any problem with power does it?
So why not cutting the spi traces and running wires only for the spi?
It might not be elegant but depending on the pcb it might be workable (ie, desoldering something and putting an spi only connector glued to the board) or at least it works to test it.