to the OP. my suggestion is to try running it like this...
axe > matrix > NL - with cab sims on
axe > matrix > whatever cab you're using for the jcm800 - with cab sims off
don't try to compensate for overall tonal bias by using the amp controls. what i mean is...if everything sounds too bright, then use the global eq to correct it, not the amp controls.
also - don't touch the advanced parameters. at all. you shouldn't need to. if you cant get a great tone just by using the basic amp controls, then something else is messing up your sound and no amount of advanced tweaking will solve it (as you've discovered).
simply changing the cab (real or IR) that you're playing through will affect your tone more dramatically thatn anything you can do with advanced parameters.
my feeling here is that the matrix cab is the culprit. i bet if you run the axe into the matrix and your real cab with poweramp sims on and cab sims off, you will have a very, very different experience.
sterling comments suh ! !
OP - Sim makes a very important point here…
the eq controls in the amp block basic page are 'tone' centric.. wind up the presence for example and you'll hear the extreme highs get fried [which may or may not be a good thing.. that's up to you]..
however, if you feel [using the example above] that you have basically the right tone [gain wise] but would like to strengthen or calm the extreme highs, either go to the amp block's eq page and fine tune it in there, or pop a GEQ block after the amp and fix up the EQ there..
the NL cabs can be very bright.. I think this is what's doing the damage in your case..
the NL's are superb cabs, but they're nothing like a traditional 2x12 cabs.. they are something unto themselves and so need to be treated as such.. especially with respect to EQ..
jack your real 4x12 into the Matrix..
if you have a pair of 4x12 cabs, even better.. jack them both in, hook up in stereo..
then shut off the cab emulation in the Axe.. this will be more like the playing experience you are used to..
so then crank it and go wipe out the street..
and then hopefully your next thread will be "OMG and I was going to sell it!!"