It could be a few things. Unfortunately, all the easy things are ruled out at this point.
There could be a small amount of drag that you can't feel when moving the head back and forth manually but it's enough to cause the motor to require too much current to move when it's at full speed. You cleaned the rails but it could be one of the pulley bearings or even the bearings that ride along the Y bar.
The motor itself could be bad which is rare but not unheard of.
The motor driver chip on the main board could be malfunctioning and causing the current issues.
Although it seems like the encoder system is working, it may be intermittently misreading the encoder strip and the error adds up to a problem. I'd expect an encoder error with this but since the systems are connected, they can cause weird errors that don't seem to match. The long trailing cables could be failing which would also mess up the encoder data as well.
Unfortunately, there aren't really any more advanced electrical troubleshooting guides to narrow it down. The Mutoh manual will just tell you to replace the parts and hope for the best basically.