I'm not sure, but isn't the whole point of using a disortion pedal NOT to get a clean sound? :P
In my eyes/ears a Marshall wont give you the Floyd-sound, if it's that your'e after. Remember, a clean sound is essential before you put on any effects.

About that other thing. The same thing happens to me, when I have a lot of gain on my JH-1. But I have stock pickups...

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Whats, uh.... The deal?