I never noticed any tone difference between a string-through guitar and a FR equipped guitar. That they do have less sustain etc is a fact though. Why don't you really like EMG's? Anyways, when using EMG's always do the 18volt mod. It's super easy, just use 2 batteries in series instead of 1, so they run on 18volt. When you have the possibility to stuff two batteries in your guitar, do it. It will increase the headroom, things will sound more clean and not as compressed or clipped. More dynamics.