Okay, this might be the answer. So I switched pitch and PEQ blocks, placing the PEQ before the pitch block. This time I forgot about trying to match by ear the overall tone of the non-pitch-shifted guitar, and just went by ear with the PEQ to get it to sound best for the part I had looped. I came up with a ridiculous scoop, approaching kind of a single-coil type tone that I think works for this. The result was that, at least with my guitar, the tone ended up sounding much more natural. I actually ended up decreasing the VC Tracking Adjust to 1.49.
I think posting presets is Pandora's Box, because I know many presets created by others sound bad with my guitar, so I expect that presets I post will sound bad with most people's guitars. But I do think that regardless presets always serve as a deductive tool to figure out different ways to achieve the tone that works for you.
Anyway, I don't know if anything can be done to maintain a natural pick attack as you shift downward to emulate a 7-string, but if possible, that would be awesome. Again, I may just be missing something. I was wrong about something once before at least (I think that was in the 80s), so I may be wrong here too.
By the way, I know the example I've cited, A Change of Seasons, is not exaxtly a bunch of arpeggios, as I keep citing. Something like the intro to Beneath the Remains by Sepultura would be a great test in this regard, just shifted to whatever, since the original is in E standard.
But of course as you shift downward playing clean you are really trying to emulate a baritone guitar, then, as you go lower, a bass guitar, and the tones for those are going to require different input signals. The physics of a long scale length, for one, aren't going to be represented just by a pitch shift, so as I reason this as I write, it makes more and more sense as to why you'd want to apply aggressive PEQ to your dry signal before hitting the pitch block, to have a signal that emphasizes all the important elements of the part you want to play. In the case of this Dream Theater example, it was the girth of the low B with the pick attack. Of course there's some gorgeous compression going on in the original recording, but I'm not even getting into that, and I wasn't at all trying to match the actual tone of the recording, just trying to get something to sound natural at all.
