Thought I'd give an update on where I'm at. Thanks everyone for the help and suggestions! Really appreciate it
The explanation about the spine reflections makes sense. It's a bummer I can't get rid of them completely, but fortunately they only show up in my worst case scenario tests. Thanks to my shoddy construction skills I managed to chip and scratch my glass so I'll probably have to replace it. This time I think I'll talk with some local glass shops rather than my hardware store. Some of them carry some reasonably priced anti-reflection glass from Tru-vue and I'll be able to actually miter the glass to 50 degrees this time. I'm aware you can get some odd results if the AR coating starts to rub off, so I might just go with regular glass again.
I'm using the stock 16-50mm lens on the Sony A6000 which has to be zoomed to 25-26mm every time I power them up. This fills the frame with the cradle wing as recommended in the calibration instructions. I'm still trying to get the calibration dialed in. Since I'm aiming to scan a ton of yearbooks, I want to keep manual de-skewing to a minimum. I don't think it's possible to get it 100% perfect, but fortunately Lightroom's transform tool works great and can be applied 'en-mass to all the appropriate images.
As for "regular" books I've definitely hit production level with those. Got a few scanned in this week while playing with Pi-Scan and have been getting excellent results in conjunction with ScanTailor Advanced. The BW processing, margins, and various auto corrections make most of my precision pretty pointless haha, but the results are great
One note on Pi-Scan though. It doesn't really play well with A6000's. When it works, it works fantastically, but the connection can be finicky. To connect I have to turn one camera on (no cameras detected), turn the second camera on (detects the first camera), then turn
off the first camera (detects all cameras), then turn on the first camera (camera doesn't see connection), and finally fire a test shot (both cameras will sync up and fire). During shooting I've had one of the cameras (both have done it) drop out which causes Pi-Scan to hang after pressing the shutter. I've found that disconnecting and reconnecting the USB cable and then shooting another shot fixes this issue, though I have to make sure to shoot the pages again as some pages will be missing in the end otherwise. I've also fixed it by rebooting the Pi and disconnecting the cameras and removing their batteries, but I think the aforementioned method works consistently. Whatever this bug is, it seems to have defined parameters that I'm learning to work around. I'm unsure as to the root cause. Pi-Scan is using a slightly older version of gPhoto, but the Sony A6000's tethering isn't the best and the camera itself might be causing the problem.
In any case I'll spend the next week\weeks figuring things out and report back with what I've found and some examples of what I've got dialed in with the lighting.