Play with the tones on the amp and the guitar. It's about fine tuning it for each guitar you use. Modeling amps are nice because you can have presets. I keep a log for a few of my amps on what settings sound best with which guitars. That way I can always get back to something for recording. If you still can't get what you want, you may want to play with the pickup height. I'd do all of that before you try to start swopping parts out.