Thanks for the post. I am looking forward to having the volume levels equalized.
I do have a question that I hope someone may be able to help with. I am running my JTV-69 with a HD500x and the acoustic side of it is a big frustration for me. I am getting a horrible resonance form certain frets. A String - 8/9 frets and the D String 4th fret. There is such a deep unpleasant sound that comes from the guitar. I've tried so many different patches and no luck. I think it's the guitar.
I have a JTV59 / HD500X that I use a lot for acoustic sounds. I also have had issues with resonant peaks on my JTV. I have a pronounced peak at F# (D string, 4th fret), just like yours. My 59 is a very resonant guitar, which is a good thing, but it screws with the modeled sounds. I have used HD Workbench, to turn down the volume of the 4th string a little to reduce the peak on that string. As Elantric said, using heavier gauge strings also helps with the acoustic models. I don't believe I have a physical problem with that fret, but I'll have to inspect it closer to be sure.
I'm not sure how else to deal with resonant peaks like this except maybe to use a notch filter right at that frequency.