Thanks sharing the luv, that is, the results of your rethinking/reworking, here for everyone's benefit! There's a working player in my town that has always gone to great lengths to cover up or otherwise hide his gear so no one will find out the "secrets" to his special sound. I just roll my eyes.:roll
I've added the PEQ setup to several of my presets and they all sound better, except for my George Benson type jazz sound which still needs a little tweaking. Which got me wondering how you even thought it was a good idea (and why it works so well)--boosting the very frequency (and it's octaves) that the tone stack was designed to heavily cut...
Do amps wish that guitar PUs were more mid-rangy? The result speaks for itself, but the logic is baffling to me.
Mixing trick. Just used a technique that I normally do in mixing but applying it before the preamp, which I've never tried. I tried it and it worked really well.
For darker jazzy type of applications like you are discussing, just use a lower number on the top part (band 4). Use a multiple of the tone stack, ie. if the "tone freq" is 600hz, band two would be 300hz so add them together instead of doubling the 'tone freq'; in this case it would be good to start at about 900hz. Then adjust by ear. The bigger key was the Q settings, which were JUST as important to making this work in the end. I spent some time critically analyzing that by ear. Depending on where you end up on the higher band, you might have to tighten (raise) the Q of the curve to make it work.
There's as much art in this as science, so always trust your ears and not just your eyes.