Okay, I haven't been able to test with a ton of IR's but I think I found the answer, which I detailed in this thread: https://forum.fractalaudio.com/thre...frequency-instead-of-changing-pickups.192601/
I first tried the newer wiring posted from Awesome Guitars, and it was definitely wrong; it was cutting out a coil, or out of phase, or something; I kept taking off the pickguard and putting it back on to see if I had screwed up the wiring somehow, but it was right every time; it was just a totally wrong, probably out of phase wiring. It's definitely mislabeled. So I re-rewired with a modification of the old wiring, but with one coil going into the other going the other direction. I cannot tell at this point which is actually North and which is South, but the rewire did actually sound better. The thing was, I was so frustrated with that pickup and the mislabeling, and the enormous time I spent troubleshooting for no good reason, I just decided to try something else I had been considering for some time, and that's what I talk about in that thread.
The best pickup swap I've ever made was with my Washburn Trevor Rabin, where I replaced the stock JB/59 set with a set of Saturday Night Specials. I had tried those Saturday Night Specials in my Sun Valley Super Shredder before, but they just sounded too thin and harsh overall. But I thought about lowering their resonant frequencies to be pleasing with this guitar.
The immediate result was that, with the handful of IRs I grabbed, I was starting to get the effect that Leon Todd and Brett Kingman have in their videos, where they just grab an IR with no smoothing or proximity, and they get world-class tones right away.
So, my guess from this is that, when you cannot get any IR to sound just right without smoothing, it may be that your pickups' resonant frequencies are dissonant to your guitar's resonant frequencies. And if you tune your pickup to harmonize, if you will, to your guitar's resonant frequencies, the overtones that are strongest from the coupling of your body and neck, you can effectively remove the harshness from your guitar at the source, the relationship between the pickup and the guitar. It's not that the guitar is inherently harsh, in my total layman's theory, but that the resonant frequency of your pickup just clashes with it, and that is sooo easy to alter. I'll write more when I have a chance to experiment with many IRs to see how my newly "harmonically tuned" guitar reacts across the board.