After trying different brands and gauges of strings on my Comanche, I've gone back to the "OE" size and brand of strings (D'Addario 10s). These just seem to feel and sound better than anything else
on this particular guitar. However, Ernie Ball 09 - 42 sound and play better on my MIM Strat. Could fretboard radius and material play into this at all? The Strat is a 9.5" radius (rosewood), where the Comanche is a 12" radius (ebony). I've also noticed that I have to roll some of the bass off and lower my gain setting on my amp. I don't use much gain on the amp* at all, just enough so that it "breaks up" a little without killing the inherent tone of the guitar.*
My current amp arsenal is 2 FENDER Pro Tube Pro Reverbs (2003 & 2005 respectively). Upgrades include all JJ Tubes and Eminence Cannabis Rex speakers. Since the speakers have broken in, I'm getting some pretty sweet tones out of this combination.
I also have a FENDER Super Champ XD with a 10" Eminence Rajun Cajun. I can get this little guy almost dialed in to where it sounds like a "junior" version of my Pro Reverbs
*I use less gain and more volume to give the amp a "pushed" sound.