Ok, I am on a proper computer now so this should be far less of a hassle.
Yes, everything is a compromise with strengths and weaknesses when it comes to guitar equipment. This is why I have a Les Paul with an A-Bomb bridge and a Rebel Yell neck as well as a Godin LG with a Rebel Yell bridge and VHII neck, and a Godin Redline III with a Juggerset 6 and an Ibanez RG7421 with a Juggerset 7.
At the end of the day, compromises don't really make for an instrument to shine in any one way. IMO, I try and match pickups that best suit the temperment and tonality of the sort of instruments they are mounted in.
Godin LG is dark and low mid focused being a solid lump of Mahogany instrument with a mahogany neck and rosewood board. In this case, the super bright Rebel Yell bridge pickup and the lower output and warm, but almost single coil quality of the VHII goes REALLY well. With coil splitting, I get from Hard Rock and even early metal right into wonderful classic and blues tones.
Gibson LP Standard. This 2002 LP Standard is a swiss cheese instrument with a boomy neck position and a thin bridge position. Originally housing a rebel yell set, I needed something that would work better with a one channel amplifier. So, to try and balance the pickups, I decided to go with an A-Bomb to phatten up the brdige pickup. The result was great. I actually prefer the Rebel Yell because of the great lead feel and the nice wide pick attack, but the A-Bomb just has extra push to sound really phat, round, pissed off, and snarling in that guitar. It really pushes a LP to the edge of any sort of traditional LP voicing but the essence of the LP tone is still there and the throaty roar really compliments the natural midrange lunk of the instrument.
Redline III: Basically, this instrument is a darker (Balanced sounding) strat with an LFR trem. When I heard Misha talking about his signature pickups I originally bought this instrument on the cheap so I'd have a piece of wood to put them in. I am a huge fan of Godin as a guitar manufacturer, and my trust was not misplaced. The pickups sound dark, powerful, huge, and phat in this guitar. There is also a bit of this scooped mid quality to the tone which I thought was endemic to the pickup design, but apparently I was wrong. 'somewhat'.
I originally tried Misha's wiring with the guitar but I recently tried Ibanez style wiring on my RG and I really have to go with that. It's just superior for what I do and the neck pickup in parallel gives access to those more classic blues type tones. I currently have 331pF ceramic disc capacitors on order. I had to buy like 20 so maybe if anyone here wants some, I could sell them for like $0.50 + shipping haha.
Ibanez RG7421 (Made in Japan) The prestige line, before it was the prestige line. Fabricated in Japan, this was probably the best built guitar I had ever played, but with terrible pickups. When replacing strings on the Redline III, I heard how good the juggernaut set sounds at lower tunings so I just had to get a 7 string.
Well, gone was the theory of the hollow mid tone; that's just with certain wood types. These pickups gain a lot of attack, articulation, and upper mids when combined with a maple bolt on neck instrument with a basswood body. The wood recipe misha likes results in a great fit with the guitar. i.e. the way the pickups were intended to sound. They still have a purring top end but they have way more attack (Djent?) and twang in the upper mids and they still sound supper phat and smooth. As mentioned, I got introduced here to Ibanez wiring when I had a conversation with Ben French. And, it's awesome.
Neck (series) (Parallel) Neck and Bridge (Series) Inside Coils tapped Bridge Parallel. Along with the 331 pF cap on the volume pot and a lower value capacitor on the tone pot, the range of tones this setup can produce is staggering. Sometimes, some of the best tones can be had by dialing back the volume and / or even adjusting the tone.
Well, I think the key here is to possibly go with what appeals to you the most sonically and in terms of feel. For other applications you may want to think of expanding out to a different guitar to cover the most ground.
If you want to go the A-Bomb and Rebel Yell / Emerald / Cold Sweat / VHII route with your PRS, maybe you should pickup a used Ibanez RG621 for a second guitar -in due time-, and swap the stock pickups out for Bare Knuckles. (Or maybe MIJ RG7421 or RG7621. Just note that with a 7421, the pickup cavities will need to be routed)
If you want to try Juggernauts in a PRS, maybe you want to track down a used Godin LG and put an A-Bomb / Rebel Yell combination in it? I can tell you that this pickup combination would sound ludicrous in this particular guitar design. Huge and immense. Or, I LOVE the Rebel Yell Bridge and VHII neck in that guitar. Or, get a Les Paul Studio used for Rebel Yell & A-Bomb goodness?
But so far, based on listening to the clips and our conversations surrounding this exchange, I would recommend the following:
Since you typically use BRIGHT amps and you roll off the treble to smooth out the sound, go with Juggernauts. They naturally have a bit of a rolled off tone in the upper mids with a nice bite in the presence. I think their natural tone, dynamic articulation, and note compression would go very well with the sort of amps you play.
I strongly recommend the treble bleed mod to the volume pot (s) and you can run 550k pots at least. Open up the top as much as possible!
The neck pickup is articulate and is pretty much a more powerful version of a VHII. It's not a shredder's pickup and it should get you in the ballpark for what you want for blues tones. When split or run in parallel, it will be somewhat stratty but the effect will obviously be enhanced if the pickups are installed in a fat strat or in a super strat. With the PRS, it will still sound like a PRS. More importantly, being able to roll back on the volume pot to reduce output will really help take the 'contemporary' edge off of the sound.
The A-Bomb set is awesome but for you, I just don't see you getting anywhere near Plini with them. It's just such a different voice. More like this, perhaps:
https://www.youtube.com/watch?v=3mjtsXaYRV8
