Okay, so I reseated all the pins and things that you highlighted. No go. Even made sure they were all hooked in the right way round, in case some doofus got them backwards. No mods, as far as I can tell. No extra wires or boards. Sure enough the board above the drive mechanism says "Analog BD". The sideboard says it's revision A.
I devised a method to measure speed, primitive as it is: I marked a mark on the flywheel and filmed some video of it spinning, then compared timestamps before and after 10 rotations. Some maths gave me the number 4.76 rotations per second, or 285 rpm, within margin of error of the intended 288 rpm, so it's not the speed, I don't think.
I also noticed that when attempting to load a program, there wasn't any noise. When I loaded anything from my floppy emulator, the computer would make constant beepy noises, however, when using the actual drive, all I got was a singular boop when the drive head re-zeroes. Perhaps this is significant? What it seems like to me is that the drive is not seeing/depositing anything on the disks, either that or it's not telling the computer anything about what it's reading. IDK though, I'm a bit of a noob at all this...