Summing up the methods it took to solve the transient voltage problem 

1. All wires are shielded and terminated to common ground. This combines the ground between welder and robot.
2. All electric lines follow a parallel path. An example would be having the welding return follow the torch input line. In all my years of welding this is the first time this technique has been needed. 
3. To be used in industrial environment the current generation of low voltage motion control drive boards for 3D printers will need some form of protection circuitry between the board and motors and/or limit switches. Preferably as close to the board as possible. In my case there was a direct path from the limit switches to the processor chip. The surge at welder start up created a voltage spike in the switch circuit and caused the processor to reset.