There are many issues to consider when dealing high voltage pulses. Making high-voltage measurements can be hazardous to the equipment, and the initial setup was designed to protect the controller input by using limiting diodes.
Later you have discovered problems using the serial interface (this can create a path for high-voltage pulses to the external equipment grounding) and in order to eliminate such noise we should provide an insulation barrier by using isolated measurement devices between the equipment and hazardous voltages. Electrical isolation pertains to eliminating ground paths between two electrical systems by breaking ground loops which are the most common source of noise in data acquisition applications.
There are three basic types of isolation that can be used in a data acquisition system:
-Electromagnetic isolation (uses a transformer to couple a signal across an isolation barrier )
-Optical Isolation (opto-couplers)
-Capacitive Isolation (Capacitive coupling )
We have chosen the electromagnetic isolation by using a separation transformer because that it is very simple to implement, yet practical application requires more attention to the correct execution of all connections.
A good pulse transformer should minimize parasitic capacitive coupling, so it needs to use separated coils with low number of turns (as I have presented in the previous attached pictures).
Not to repeat the same mistakes we should first need to know where and how have you connected the wires. It is critical that this ground wire connection is properly done to the chassis, and it should be as short as possible. Maybe it will be necessary a weak coupling between the induction coil and the measuring probe, so this time try lowering the number of turns up to the limit of capture the necessary pulses.