HI Guys.
I recommend leaving the isolator in to keep the LED noise currents out of the Amp input. The transformer stops LED any current from flowing on the ground of the audio cable. If ground current exists, the current will couple into the L+R audio +inputs.

I agree with rerouting the audio cable. Move the cable out of the bundle it's ty-wrapped to. This will prevent other LED noise from coupling into the cable. (Thanks to Dave for finding this).

There are two methods being used to get the audio from the CPU board to the isolation transformer.
#1. Female connector that is pressed onto the audio out header connector on the CPU. (Shown in the pictures above)
Keep an eye on this connector. If you find that wiggling it makes the audio cut in and out then you have a poor connection. I recommend swapping the cable to method #2.

#2. Later games tap the audio out on the 3.5mm Green connector on the back of the CPU. It's a better connection (IMO) BUT it's not perfect. Wiggle that connection and if your cabinet speaker cuts out then your connection is not great. Some of the 3.5mm audio cables used have a slightly smaller diameter ground barrel and this causes the ground to open up causing static noise in the audio and the cabinet speaker output to drop. Position the cable so you get a good connection for now.
Thanks,
Mark

The cable should be shielded but I have not dissected one to make sure.
A shielded cable will not help with magnetic coupling. It will help with capacitive coupling.
Here is how I understand it. A magnetic field in proximity with the shield of the cable will induce a current on the shield of the cable. In this case, the voltage difference across the ground of the CPU board and the Amp causes a current to flow in the ground shield of the cable…which may couple onto the L+R audio lines.
Even with the isolation transformer in place, there is still a small ground loop present through the L+R input impedance. I suspect this is what might be picking up the other noise.
I did some testing on my machine and I did get a good reduction in LED noise when I used the isolation transformer.
I suppose there may be cases where it behaves differently. I'm open to understanding how and why.

One more question. Does your game sound reasonably loud when you set the volume to 30?

Thanks,
Mark

Signal Volume.
I'm running my System volume at 30. That's about my comfort limit in my basement.
I don't hear any noise at that level.
I'll play around with my cable the next time I have the glass off.

Well sound like you are in good shape.

Thanks,
Mark