Even though the pickups are an upgrade from the original INF's, perhaps your pickups and the body are just not getting along. Evo's are made to favor upper-midrange frequencies so they'll even cut through with basswood and
alder body guitars (2 types of wood known to mellow out and attenuated highs a little bit)- now put a pickup made to behave that way on a big old slab of maple- a very bright wood that is very much unlike basswood or alder- and you're probably going to have a harsher tone than you really wanted. The fact that it's a maple neckthrough means that the maple is going to have the bully-pulpit tone-wise over the mahogany wings.
What would help is to counter-act the tonal properties of the wood with pickups better suited. You may want to try a
bridge pickup with a less high-freq-favoring EQ curve. Perhaps try an alnico-magnet pickup over a ceramic, which IMHO balance better with maple and mahogany. You shouldn't have to mangle your amp EQ to get an acceptable sound.
