Well, a number of solutions.
1.) instead of boosting the treble and mids, try cutting the bass. This ought to give you a more balanced tone, without the shrillness you're finding when you switch over to the Fred. It looks like you have everything boosted in the EQ section, so maybe start again with a flat EQ and instead of boosting to get a tone, try cutting some frequencies. Then try a mix of boosting and cutting... Then, have someone who knows nothing about guitars set the tone knobs into a configuration they think is "pretty," and see how it sounds. experiment!
2.) Either lower the PAF under the bass strings, or lower the Fred under the treble side. Basically, you want them pretty even across as a neutral starting cross- make sure they're level first. Then, experiment a bit with slight tilts in the pickups- check both string-to-string balance (by far the most important consideration) and tonal response as you do this, of course.
3.) Back off the gain a bit. More gain nearly always equals more mud, and you'd be suprised how much "heavier" a slightly cleaner tone can sound. As an added benifit, as you begin to clean up your tone, you can no longer rely on the amp's natural compression as much to compensate for bad technique, forcing you to become a better player.
4.) Lose the DS-1. Yeah, Steve and Joe both use them... but this is YOUR tone we're talking about here, not theirs. What sounds best to your ears is what's important here, and adding a outboard distortion between your guitar and your amp can definately give you excess mud. Alternatively, dial up a nearly clean setting on the DS-1; these guys use it more as a slight overdrive, to kick their lead tone into high gear, rather than as a substantial gain boost.
5.) Re-evaluate your tone in a band setting. The fred might be sounding shrill unaccompanied, but just maybe against bass and drums it'll be "that" tone, and occupy the space the other instruments are leaving open. the secret to a huge guitar tone isn't actually in having a tone that sounds massive, but rather a tone that sounds massive in context. Everything's relative.
6.) Give up and mail me that JS
, and buy yourself a nice, un-shrill les paul. :P (actually, on a more serious note, there is still the possibility that maybe a JS
into a legacy just isn't the setup for you- try some other gear and see if you like the results)