Scale doesn't change the EQ like that IME. The construction, glue/finish, and electronics might do that. I'd disconnect the tone first. If that doesn't do much, I'd check what value the pots are and first replace those. Next you could swap pickups, but it would be better if you could try one of the pickups in another guitar first. Because if the pickup sounds good and it's the guitar making them sound bassy, then any replacement will have the same problem.