this preset has a few interesting things going on. it also has User Cabs, so i can't really tell what you're hearing because I don't have those same User cabs. do you know what IRs they are?
first the Pitch Shift to detune the whole guitar is after the Amp and Cab. this typically sounds better before amp and cab, usually first in the chain really.
also the Wah block has the "Offset" parameter for the modifier turned up a bit, so you can't totally get to 0 on the Control knob. this isn't interfering with the Auto-Engage for me, but not sure why it's turned up. it might be causing your Wah block to always be on though, so i'd check if it's Engaged all the time when you're hearing the bad sound. a Wah always on when you don't expect it to be has been the cause of many "it sounds bad" problems. i'd probably delete the block (and don't save) to test if removing it solves things.
in the Cab block, i don't have the same User cabs as you, as i mentioned, but Slot 4 in Channel C is turned down by -36, so you aren't really hearing that at all, and it seems to be the same User slot, so you probably can just Mute it.
for me, Scene 4 is very close to clipping, and Scene 5-8 are all definitely clipping. you need to reduce the Amp Level parameter a bit for the Amps in those Scenes (some Scenes share amps, so only need to adjust it once). use the VU meters on Hardware Layout > Zoom out to help you prevent clipping. for me, Scene 1 is a good volume, right at the Level Set line (the line to the right of middle).
if the Wah is turned on in Scenes 4-8, it definitely clips a lot worse. so i would guess that your Wah is on all the time. i'd delete that block (replace it with a Shunt) and see if things immediately get better.