Define controller board.
Bad Nicad battery on the mother board?
Bad axis drive board?
Bad I/O board to the floppy or hard drive?
You are correct in that the original Dx had a 486 mother board.
You could dumpster dive for a replacement but what would go bad next. The BMDC is a slow board and you need a slow mother board to talk to it.
You may have a Cutler Hammer control that already has a half size industrial mother board.
The replacements are purchased from ADVANTECH. They are not cheap.