Ford states NOT to mix them.
3C3Z-9E527-AA (Original C91 injector) was replaced in 2003 with part number 3C3Z-9E527-ABRM (C94) and then later with 3C3Z-9E527-AE (C95). These part numbers were for engines built before 9/22/03. The latest injector number is 4C3Z-9E527-AA (C2 or C92) for engines built after 9/22/03 . The difference between original C94 & new C95 was internal change to clevis. Had to do with plunger suffering from side loading which then causes raw fuel to flood and enter the engine oil crankcase. Design improvements aimed at preventing scuffing.
There are no physical fitment differences between the injectors, but best not to intermingle them.
Along with the clevis re-design mentioned above (which helps prevent scuffing) one additional change below:
Change in JANUARY 2004 from the 2003 design:
DLC (Diamond Like Carbon) Coated Plunger
• The injector plunger has had a DLC coating applied to it
• The coating will further increase the robustness of the injector against poor fuel quality/water intrusion and will reduce the risk of internal scuffing.
Note: The two injectors have different operating characteristics and DLC injectors can not be interchanged with non DLC injectors.
Installing the incorrect injector could cause Erratic or rough engine operation.
http://turbodieselforums.com/downloads/6.0L 2004 Book.pdf
page 27 of the presentation in the link above