That "supertune", "super mod", "swing mod", whatever you want to call it, is just a cap and resistor. Yes you can leave it in with the MOSFET mod. However, you may have to change the value of the resistor to adjust your carrier. Most of the time the mosfet replacement by itself results in about a 2 watt carrier. There are procedures all over this site on how to raise that carrier back up to 4 or 5 watts, which usually sounds better. Sometimes that "supertune" is done in a way that lowers it down to 2 watts or so...which means you may end up with a really, really low carrier. After you do the mosfet mod, put it on a meter to see what it's doing and then make decisions from there.