Put a JB in a Jackson Soloist for reference. I can think it sounds decent but most of the time I don't like it.
A similar thing happens with a Les Paul Studio with stock 498T. I use this guitar for reference a lot.
A pickup that sounds grate for me almost always is the Wagner Godwood. This is...
Apologies for not being clear.
It is a mod to the amp.
It allows the user to set the negative feedback in the power section.
Makes the amp have more tonal range.
Swapped the 5881 for EL34 for a test and found that the amp sounded more like your clips. Lost some of the girth but gained some clarity in the highs. More like a Marshall for sure.