Audiorader, I am not sure this is even important, but when you say that the problem switched from one side to the other after you switched the pairs of leads at the cartridge clips, do you mean as measured by the Foz or did you also listen to some music and confirm that the lower output problem had now switched to the opposite channel in your whole system?
Apropos of the question of phase, I agree with Dave and Atmasphere that this could be the issue. One wonders whether your headshell is miswired so that in one channel the "hot" clip is really going to ground in the preamp, and the "ground" clip is actually going to the hot pin on the RCA plug. Thus all could appear to be correctly wired while in fact that one channel is out of phase with respect to the other. This defect also does serious damage to bass coherence and stereo imaging. It's hard to listen to, in fact. If your tt, platter, and tonearm mount are all level and plane parallel to each other, then phase error is a possible cause.