[Mark Nixon]

You're over thinking it.

The distance from the BOTTOM of the injector bore UP to the quill tube entry point is the same.
The change is ABOVE the quill tube entry point, ergo machining the bore ABOVE the quill tube will NOT affect the quill tube's positioning in any way.

The truth is that the 6.7 injector won't seat in the 5.9 head simply BECAUSE the bore is too tall ABOVE the quill tube.
If you were to try to install the 6.7 injector in the 5.9 head as it is now, the quill tube would probably tip UPWARD to meet the feed hole and I know for a fact that the tip would leak compression past the copper washer.
Machining the top of the bore will correct the problem.

OR you could machine the bottom of the locator ring on the 6.7 injector body, which has also been done to correct this.

You have the parts there, do some measuring and looking, then come back and tell me what you find.

Mark.