Go for a chambered body to get a little more weight, ironically, to your tone; it'll help with the flat top body and, I'm assuming, top routing. Even if the guitar is rear-routed, having the body chambered will help nail that typical thick-mahogany-bodied tone.
Consider a rosewood neck, or at least a rosewood fretboard. Bolt-ons are inherently a little brighter than set necks, especially for the neck pickup, and having the neck made of such warm woods will help a lot. My experience with Warmoth's conversion necks is that the 'pro' conversion, with its hefty truss rod, brings through the highs very clearly and a super-warm wood like rosewood will help curb that a little.
Ditch the Bare Knuckles. Aside from being ridiculously overpriced (there's a hundred and one other boutique pickup makers that do the same—if not better—job for less), they're going to be too bright. You don't get the thick, iconic PAF tone by putting PAF-copies in a flat-top, bolt-on guitar; you need to go for pickups that are wound even thicker. You could of course get somethind wound specifically for you by any number of boutique winders, or even the Seymour Duncan Custom Shop (having dealt with them myself recently, for a similar tone in a similar guitar, I can attest to their ability to deliver), but for less bank-murdering options, try DiMarzio, the kings of getting thicker tone out of thin guitars. Try the bridge version of their PAF copy as a neck pickup, and for the bridge try an Air Norton, or if you don't mind bumping up the output a little (though it's still a barely-hot pickup), a Breed Neck. Seymour Duncan Pearly Gates, or '59s with A2 magnets, are also good options that I've had good experience with in the quest for classic rock tone in inherently modern-sounding builds.
I'd also suggest you lose the stainless steel frets and the bone nut, as regular fret wire and a graphite compound nut will give you a smoother tone. These do of course have a much bigger impact on how the guitar plays, though, so I wouldn't consider changing them a priority.
One thing that is easily overlooked is the pot value. Most people just go for 500k for humbucker and P-90s and 250k for Fender-style single coils, but Gibson themselves use a mixture of 300k and 500k for warm guitars and just 300k pots for brighter guitars. Sticking 300k or even 250k pots in PRSs is also a very popular mod to get a more 'vintage' tone out of the slightly more modern design. I would recommend you go for a 300k volume pot, at least, with a 500k tone.
Lastly, I'd suggest a tiltback neck. The break angle over the nut is important for those classic rock and heavy blues-based tones, especially on the plain strings. String retainers can help on a straight headstock, but a tiltback makes it easier and more consistent; some people would say the 3x3 tuner layout is important too, though this is a needless step too far, in my opinion.
... and if in doubt, get an EQ pedal and just pump the mids up. Always a nice, quick-n-dirty fix :icon_thumright:
