Other than the bridge / saddle / mute of the "original" 4001 / 4003, and the twin truss rod malarky, as have been mentioned elsewhere, something else that could do with changing is the height adjustment of the neck pickup.
The scratchplate is a thick piece of plastic, so the neck pickup can't physically be set more very high, even if you take the springs off (I have). It'd just make it a bit easier resting my thumb on it.