The above example are refering to people wanting to use 954 CPU with the 929 wiring harness which wont be compatablie but since you have the wiring harness you shouldnt have a problem (although you will need a pc3 with a custom map as the 954 cpu has a base map suited to bigger throttle bodies, 12 hole injectors and an extra 25cc among many other small differences)
And I would consider using the 12 hole injectors and larger throttle boddies from the 954 as these flow more and give better atomisation! also will make the base mapping much closer to what it should be as you have rectified one of the main varibles between the two bikes as far as the ECU is concerned!
Hope this helps you out a little!
Cheers Jai