Theories why the Rubicon went with D44s vs upgraded Dana 30/35?

Stubs are the same relative to each axle family as per my comment above about helping Revolution make the JK joint axle kit for the TJ.

This will solve most of your dilemma.

2 of these are JK ball joints, 2 of them are TJ ball joints.

View attachment 66736
different design but without a micrometer the diameters do not look different. i'm sold, same but different.
 
different design but without a micrometer the diameters do not look different. i'm sold, same but different.
Yep, same but different. The main difference is the taper, that's it and that same difference also exists between the WJ and TJ lower ball joints. A micrometer may tell the whole story but it is easier to know that you can swap them between the inner C's with no difference in how they fit the holes.