One thing more I've discovered about this guitar: the Schecter Sunset Strip bridge pickup is now reminding me of a Duncan JB, in a bad way. For the tones I love, I find that I get an ice pick pick attack right at 2284 Hz. I've been dialing this out with Input EQ (Q at 10) on the amp block. I have a Washburn Trevor Rabin that came with a JB in the bridge and a '59 in the neck, and it had the same problem; on that guitar I ended up replacing both stock pickups with Duncan Saturday Night Specials, and those work beautifully for a balanced, well, beautiful, output that, to my ears, works well for virtually any genre, any tone. It doesn't hurt that I wired it for series/split/parallel for each pickup, so it's a Swiss Army Knife of tone.
This perceived harshness is a problem for some people with particular ceramic pickups, and sucking out the harsh frequency is quick enough. Hell, one could just throw a Filter Block with the same channel right after the Input Block for every preset, but I'm still adjusting the amount of that frequency to remove with each tone anyway; regardless, the AF3 makes this ice pick easy to mitigate.
To the root of the problem, a fix for the JB for those who hear it the way I do is to lower pot values to 250k, and I think that's one good way to approach this; if the legend of Jeff Beck's TeleGib is true, that it's the origin of the JB, and Duncan designed it specifically to go with 250k pots, then there's the explanation for why 500k can make your ears bleed. Other fixes I tried for the JB on my other guitar did not work for my ears: simply to lower the pickup further (I already go pretty low) or to lower the screw pole pieces.
I'd say that maybe I'm just not into ceramic pickups, but there's such variety out there, I'm dubious that the magnet composition alone is what's hitting me so harshly. There are so many factors that determine the character of any pickup.
Not that a JB 500k type tone is unexpected from a Super Strat; it's iconic and ubiquitous, which really makes me wonder if I'm missing something by wishing I had a damn AlNiCo II in that position. Because of this, I'm going to experiment with trying to create some tones outside of my normal workflow. I have an army of IRs I rarely ever even audition, and I tend to use the same old workflow to fashion a tone; all of which is easily fixable by me getting off my ass as a guitarist and putting on an ill fitting audio engineer's hat. My biggest problem is that I play guitar like an audiophile; if something's not right in my tone, it's not right in my playing; I can never disconnect from the sound (not that this is unique among players). Anyone know a good support group? Maybe this forum is it. I'm going to try this as a learning experience to see if I can find a way to dial in tones that inherently mitigate the harshness of this pickup, just by altering my approach. It is possible that what I view now as a harshness in this pickup is actually a strength, and if I can find a way to use it, my tone will have that much more character.