software

Well my Charvel has an active midboost in it. It can add up to 6db of boost. It's a very cool device and I quite like it... The Jackson pickup it came with was very smooth, then I replaced it with a FullShred and it was just... amazing! But now I put a Miracle Man (bareknuckle) in it and I noticed a loss in harmonics (while there should be more) and a tone I wasn't expecting. Less tightness, less bass than what I hoped for. Could the active electronics be the fault? Would it definitely sound better if I wired it more simply, volume/volume/tone with all 500K pots?

I'm not sure. All the active electronics are is a buffer. Normally that serves to negate high frequency loss caused by driving guitar wiring and cables. It sounds like you're hearing the tonality of the pickup itself.

You can try it w/ o the preamp, but the Jackson circuits are pretty transparent... it may do the trick, but I wouldn´t really expect it to

Pierre, if I were you, I'd do the soldering job again, and if the results aren't better, I'd use the guarantee and have the MM changed for something else, or in the worst case I'd have my money back.

However, it's difficult to imagine that a scatterwound 17.5K pickup with a large ceramic magnet has less tightness and harmonics than a 14.6K Alnico V pickup. Ceramic magnets are so much more powerful, tighter with the bass and more aggressive with the highs than Alnico V.

It could be though, that scatterwinding eliminates artificial peaks in the frequency response of the pickup. So what you're hearing might be simply a flatter response of the Miracle Man, which you're simply not used to. But still... it should have a tighter sound and a lot more output than the Full Shred due to its construction.