I went back and did what you said, and you were 100% right. I went from an 80-something to 94% by lightening up on the mutes. So....I did go back and convert all the palm mutes to string mutes (most folks probably wouldn't notice the difference by looking, honestly), and now you can really choke up on the palm mutes and get that nice chunky scratchy sound, without getting downgraded. I got 96% on my first try.
Thanks again for helping me get the song exactly how I wanted it! :D
Billkwando's post in Note detection/CDLC issue on one of my customs was marked as the answer