OK...I'm still not clear on what exactly the problem is. I put an ected locker in my Ford 8.8 rear end when I re-geared it to 4.56. Because of the larger ring gear, I had to grind (create a flat spot) the center pin to allow the axles to travel far enough in to get the c-clips on. The alternative to this mod is to grind the ring gear teeth.
I choose to modify the pin instead and have had no problems. If the pin is modified correctly, it is rotated one way to remove right axle, and 180 degrees to remove the left axle. When both axles are installed, the pin is rotated 90 degrees and the pin bolt is installed so that the full pin diameter is available to keep axles at the correct position. The mod might weaken the pin a little, but won't affect axle position or locker operation that I'm aware of.