Bah. :( I say it's time to put wood filler in that neck PU route, refinish it and rock out. JK. If I recall correctly, the old Mustaines aren't compatible with other active PUs because of how they're powered or something like that. I can't remember exactly what it was or how it could be worked around, but that may limit your replacement options even if you don't care about matching or are open to putting a matching paint finish on them, taking the plating off of both, using a blueing/blackening chemical on the bare metal covers, concrete dye can also soak well into Nickel, etc.... Maybe you could spy on Tim and figure out that Camo finish for us. :P
Well good luck man, sorry you're PU is trash.