Clean I keep it pretty much the same as my other guitars, just changing the presence to taste: Also for all these settings the GEQ is completely bypassed on both channels.
Gain- 3
Treble- 5
Mid- 3
Bass- 3
Presence - whatever sounds good guitar specific.
Reverb- 6-7, again to your preference
Master- 3
Gives a good straight forward jazz/blues/whatever clean bell tone with my strat with dimarzios. Overdrive pedals sound great with these settings.
For lead I mix it up alot differently than with my humbucker equipped guitars. I try to go for that really smooth compressed lead tone like Eric Johnson or Allan Holdsworth. Most importantly I boost it with a BB preamp with gain and volume at 5, and treble and bass at 0, this really gives it more singing qualities and a compressed feel. Although you can get similar results with any tubescreamer or w/e.
Gain-6
Treble- 4-5 (depends on the room I'm in)
Mid- 5
Bass- 3 (usually kept at 2, but at 3 it seems to fatten up the highs)
Presence- 4 to 2
Reverb- 5
Master- 4
If I really want to make my bandmates mad, I set the GEQ to an almost upside down V curve, so the mid line is near the top and bass and treble are under the middle line, while the 2 and 4 sliders are at the middle. This really engages the Eric Johnson liquid tone that feels like you can just eat it up. Its cool for me, but pretty much can cut through a cement wall. :lol:
My strat is a USA Deluxe with the S1 switching and I think the pickups are hotter and not as bright as vintage pickups. I keep settings the same for all guitars and I use a DC-10 head with a 2x12 3/4 cab.
I'm using a Fender American Standard HSS (The Ash bodied option, with a maple fingerboard) as my main guitar with the DC-5 combo which I setup like so:
I keep an OD, a Compressor and a Delay on a pedalboard and between them and these settings I can't go wrong when it comes to calling up a wide variety of tones.