It's set to Miata 99-05

Should I be in "log crank and cam" for every datalog? Just realized I switched it back to Miata 99-05 and kept it that way for the last log

Flipped it back to Log Crank and Cam

Sorry- you're OK being in 99-05 Miata. I was just making sure you didn't try something weird there.

sensor works, but the signal wire going back to the MS seems to be the issue -- pin 24 on the lower DB37.

Your wiring from the sensor up to where you switched the signals is OK. Assuming you switched signals before it hits the DB37.
So now it's either a bad connection in the DB37 as Brain already said, or it could still be something wrong inside the MS3. Could be a cold solder joint on the connector (DB37) on the mainboard, or, more likely, the jumper on the board (I believe it's T_sel).

Edit: Don't forget to swap the wires back!

Board looks good to me. Have continuity across the crank wire on the harness
https://cimg2.ibsrv.net/gimg/www.mia...4c26852ea6.jpg
https://cimg3.ibsrv.net/gimg/www.mia...ab98489742.jpg
https://cimg4.ibsrv.net/gimg/www.mia...a6c66a5a16.jpg

Then I'd give R56 another turn or two. Total of 10-11 turns. Make sure again that R52 is fully CCW.
Do you have a pullup for R45 (an additional reistor connected to the right side of it)?
Are you sure that's a brain-built unit? It doesn't quite look like his handiwork.

Pullup is there. Two additional turns on r56 didnt do it. Fairly confident this is truly a Brain-built unit. He took it back for additional work after the PO connected us. https://cimg3.ibsrv.net/gimg/www.mia...03c66aa55a.jpg

Sorry- that's all I got. Over to the Brain. Pinky out.

i still think there's a break between the sensor and the MS input.