Okay so I'm no high gain guy, haven't played metal since I was a teen. However, I opened your preset and loaded LT Mix 7, here's some things I did to make it sound less "congested":
- Speaker compression from 4 -> 2.5 and time constant to 2200ms.
- Speaker drive to 0 (I almost never use speaker drive param. unless going for "broken speaker sound"
- Reset XFormer Drive to 1.2 which is default for that amp.
- Turned OFF Cut and Input Boost in the Preamp page
- Turned Master from 3 -> 4
I have Yamaha HS-8's so very similar, however I tested this with a telecaster and if the input boost was too much for that, then I imagine its overkill for you're hot pickups. Try using a drive pedal instead that way you have more control over the amount and tone.
Hope this helps!