Scott, No, ball joints have no wear; mileage on car is less than 500mi. Yes, both sides have the same issue and the track width is per GT40 spec. It is as if the leading tube of the A-Arm was cut to proper length, but the width of the shoulder on the threaded tube end was not subtracted so that the entire assembly ended up at the proper length.
Chuck, the threaded shank of a rod end does not bottom out or "seat" into/against anything. The threaded tube end is bored completely through and, as it is, the rod end could be threaded deeper into tube end. However, any change in position of the rod end would take the alignment out of spec. Ordinarily, a jam nut is used to remove the play in the thread engagement (this is where the popping noise is coming from) and fix the position of the uprights upper attach point. The only rod end dimension that, if changed, would help is the distance from the spherical bearing's bore center to the top useable thread on the shank. I have checked several different brands of rod ends and this dimension appears to be standardized. Any removal of material from the rod end collar to provide room for more threads and, thus, a jam nut, would reduce the tensile load along the shank centerline that the rod end could carry.
I have tried a two piece locking collar that I profiled to engage the rod ends collar. It did help a bit, but the two screws which hold the two "C" shaped pieces together quicly strectched. The collar also interferes with the stud onto which the rod end is attached at the limits of the upward movement of the suspension and this is highly undesireable.