Did you try the center pin only Fn option?
When I was testing the YN-E3 for them on Canon 5DIII and then tried it on a Fuji XT-1 there was a problem, even in M, until they added the legacy mode that turned off all the control pins.
Since it seems to be working in TTL without the ERR it seems to confirm a communications anomaly as the cause.
I set CFn1 to 1, and saw ERR after 3 shots. Not good. So I then taped over everything except the center pin, and clicked off 25 consecutive shots with no errors. Based on the documentation, it seems like setting CFn1 to 1 would truly disable (de-electrify) everything except the center pin. With CFn1 = 1, however, I'm still seeing close to 3.2V on 3 of the pins, which is exactly what I see with CFn1 = 0.