Preferred part numbers for the male headers on the amp power board are all specified with the -A option for alignment pins; this is supposed to make connector alignment problems between power and controls boards less likely. However, current footprints in PCB are the ones without the alignment pins - either...
Remove alignment pins from part number (potentially worse alignment problems)
Switch footprints to alignment pin variants (some trouble routing traces around current sense connector)
Preferred part numbers for the male headers on the amp power board are all specified with the -A option for alignment pins; this is supposed to make connector alignment problems between power and controls boards less likely. However, current footprints in PCB are the ones without the alignment pins - either...