Without access to some debug interface that shows you what values come from the various components, you're stuck with hypothesizing and replacing parts, which is annoying and expensive. In that world, I'd also try replacing the torque sensor. I've seen it sold on Ali. I think they use a common part between multiple units but I'm not sure. I have their BB torque sensor and it seems it uses a spindle that looks like the ones used in their mid drives. They're not cheap though.
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I’ve serviced the motor before and I’m familiar with the part in question. At this point it’s not even about the cost - I just dread spending another minute wrenching on this thing instead of riding it. I’m tempted to just take it to a shop and tell them to figure it out. What really throws me off is how this only happens in the lowest gears, even though the bike has no way of knowing what gear I’m in. I even took out the Eggrider display and put the Bafang unit back on but no difference.
Yeah that part really is crazy. Obviously there's some mechanism but I don't know what. You've alreade checked change in torque and cadence as a cause. The only other thing that comes to mind is the force pointing backwards, experienced by the spindle from the chain pulling on it, which changes depending on which gear you're in and how tensioned the rear derailleur is. But I would think any such effect would be drowned by the forces of your legs on the cranks.
i had this on my tsdz2 as well as the toseven dm02, but the tsdz2 was seemingly random and the dm02 was every 7 revolutions. still no idea why it happens.