I have followed the steps you gave me, in step 4) I only removed the com.apple.logic10.plist file because the rest is working fine and I don't have any key command assigned.
Now after following your steps, I still don't get any signal from my Yamaha, I'll attach a number of pictures that may help you have an idea of what my Logic is doing.
Firstly, this is what I got when I turned on my Macbook again, but then again, I was receiving that message anyway everytime I plugged in the P-95.

Secondly, as you can see in the list of Control Surface Setup, there are a number of Yamaha version but none of them is mine.

Now in this image, I have this 01X that I clicked install on once upon and you'd probably recognise this device from the list of Yamaha versions in the previous image. If you concentrate in the Output/Input Ports you'll see there is All and Port 1. I don't know if that is correct.

Finally, in this picture is what I have found after doing what you said.
(Note: In the USB Midi cable, there are three lights, Green, Orange, Red. Everytime I connect my Yamaha it is always in Red, I have never seen it going Green. And also, when I plug the Yamaha and Run logic, the orange light flashes while the dialogue box from the first picture is displayed).
I don't know if the number of pictures were necessary but maybe, they could give you a clue.