Alrighty, so I had some success! I started off with Vimtoman's photo which got me back to disc's spinning but not reading. Got the "Please set Disc!" error...
Then I followed up with the guide LowRes posted. I used an audio disc, removed the cdrom2 from the briefcase and plugged in power and headphones directly, flipped it upside down and started making some minor tweaks to the pots until the audio wasn't garbled anymore. Tested the skips and everything seemed to be operational. Popped in a disc of Dungeon Explorer II and sure enough it fired up.
The biggest improvements came from the 102 pot. I could literally hear the audio clearing up in real time while I tweaked it. I can't tell if it's 100% perfect because I don't have any other experience with pc engine disc games to compare but this was leaps and bounds better than staring at an error screen and having a non spinning drive.
I had to search for "calibration" to find Vimtoman's photo of the potentiometers in case that helps anyone in the future. Maybe someone can add it to the calibration guide or sticky it somewhere. It's a great starting point. Thanks for everyone's help!