I put an EMG81/85 set in my Custom and initially had that noise as well as the harsh, trebly tone wash. I deduced that the culprit was the bias of my Marshall's tubes because I plugged into a friend's amp and didn't have the problem. It wasn't noticeable when I used passive pickups, but the active EMGs really exposed it. Marshall's recommended bias for my JCM2000 tubes is 90mV, and when I checked mine it was at 97mV which was way too hot, hence the harshness. I was able to get a thick Zakk tone dialing the bias down to 88mV.
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Oh man, I was expecting you to say something here. I've seen You contributing in some threads, and You're a Zakk fan too. I've seen some pictures of your guitar in some threads, and without the cosmetics changes, your guitar is the same as mine. By the Way, She looks beautiful!!! So ****ing awesome.
Now You said something that might help. I think my amp is very bright, and as You said this noise wasn't so noticeable with passive pickups. I think I will try to remove the bright cap, or lowering the bias. This might help