From the way you describe it, that sounds like maple dominating the tone. Which is not surprising, given that it's a neck-through, where the neck wood tends to dominate tone-wise :) Maple is bright, but NOT REALLY bright, usually. What's probably irritating you is the upper mids combined with that mid-spike of the JB. Maple has a lot of mids, and is tight both on the lows and highs. And yes, a lot of attack.
HD has a warmer (but not dull) top, but also a lot of center mids, which might or might not work. For J. Williams, they apparently worked, but your guitar might be different. You didn't mention the bottom end, just the high spectrum.
In general, maple (or maple neck-through) guitars get recommended ceramic pickups here. If your guitar sounds like I described, the ceramic model I would choose is the Miracle Man. I haven't personally ever owned a neck-through, so take my advice with a pinch of salt. However, it's been a proven combination here, and is great for early Dokken tone, for example. Tight but big lows, no nasality in the midrange and aggression (but not too much) in the highs.
-Zaned