How to isolate a PCB circuit from a high noise source in the nearby
There are a few things you need to learn;

1)   how to probe down to minimum rise time of scope , especially near radiated pulse noise.

2) what does EMC mean?

3) How is Common Mode (CM) interference avoided with balanced wire pair?

4) What is a Balun or CM choke?

5) Different types of Baluns as diverse as capacitors for different frequency ranges and currents. 


Where are they used?  


All Laptop charger DC cables 10k~10MHz range
All VGA cables 1~150MHz BW
Some electret mic cables 
some power cords 



What is the simple diagram? 


What is the real diagram?







simulate this circuit &ndash; Schematic created using CircuitLab

So depending on materials of iron or ferrite core and number of turns from 1 to N and ferrite mix from insulative LF to MF to conductive ferrite for  RF with more metal particles. 


the model values will change. 
Often a CM choke or CM ferrite bead just says 100 Ohms meaning lossy in band of interest.
an ethernet Balun does same job as a YAGI Balun in "fundamental" theory, but for different f , and Zo so they look completely different


5) Learn how to search for pre-existing answers on web and in this forum ( locate the search window and experiement with different keywords, tags and user names like user:me in search finds ...yourself or by exact username  user:joeblow or number user:17574 (that is I)

6) Understand that short arcs have spectrum all the way up the antenna length that fits in that length and then all the harmonics of this


so lets just say way beyond a GHz for now for a short arc from fence to target.


7) understand the spectrum of the noise interference ( and stray impedance to problem area)


Lets look at your clean 10k Pulse and assume the rise time is say 1us with 50us pulse duration then a sine wave roughly 350us , So we have almost 500MHz rise time 50KHz 1/2 pulse duration then 1 sine wave of about 3Khz


as you said this causes no problem
so that means the energy of interference is way beyond 500MHz but maybe only say some xx nanoseconds rise time.



Now which kind of Ferrite CM choke can you get?

I forgot some OP's may not want to actually learn just want a crystal ball solution.

Things to do:


make sure all sensor electronic circuits are far away from the HV generator and twisted pair wires going to the fence at right angles to the sensor STP wire pair shielded . Keep at least 10m away from the generator and wire pair to fence.


STP shielded twisted pair balances much of the spectral E field ingress and isolation distance reduces the H field current coupling 
generator and sensor wire pair at right angles reduces the antenna coupling of EMI pulses between 2 wire pairs.
use a current loop around the generator feed wire with a few turns to detect high current pulse as your air gapped current sensor into coax or STP sensor wires.
terminate the wires with matched impedance such as 120~220 Ohms or STP or 75 Ohms for video coax,
use a CLC balun or CM choke rated for RF as your signal conditioner input. This raises the CM impedance and the shunt cap attenuates it slightly.
What you want is a 1us risetime pulse and not a 1ns Rise time pulse that spews noise voltage into sub-picofarad stray capacitance.
terminate it with the matched impedance 
add more current sense wire turns or use a Rogowski coil if you are really keen but not necessary.

I have used these techniques successfully over 40 years in many applications
My 1st experience in late 70's was measuring the power of 100kA fusion arc welding of Zirc-steel tween two 4"Diameter tube
My most recent experience was measuring pulse power of a 20kV pulse inside transformer oil like a HIPOT test before the onset of corona in a 5MVA power transformer.


The pulse measures only 2 watts or 10V into 50 Ohms from a 20kV/mm dielectric test using a small 1 turn loop to coax.



(not I,  but a keen builder of HV multipliers.

This is a small partial discharge pulse measured using the above method on 50 Ohm coax terminated by 50 Ohms, similar to a small fence discharge or a Hipot bug zap. I used an old LeCroy scope to capture the image. The 1ns rise time is limited only by the scope.