I did some more experiments and might have to backtrack, in the practice I used the SD-1 as a boost, and I think that's what was causing the thinness in the overall mix. While I got the output boost I needed, it was cutting the balls.
The Holy Diver is really clear, like, imagine a combination of the Dimarzio Super Distortion with the JB, but with very clear clarity, no extraneous distortion noise, all the strings really stand out in a chord, and there is fluidity that is not created out of sheer output. The drawback to this is that yes, it's less output overall. And on my Marshall JVM 410 HJS, it's not quite enough to get the OD channels into the healthy saturation that I want. Cranking up the amp gain just gets bassy and woofy.
Should I be trying a clean boost instead of an overdrive to get that output back? Will that help tighten things up? I'm thinking of something simple like the EP Booster here. I've only ever used the SD-1 but I want to retire it because the SD-1 through a Marshall is such a staple recognizable 80's sound that I just don't want anymore. And with the new pickups, I want to retain some of that 80's vibe, while getting fresh tones.