We built a 3 nL flow cell for measuring peak profiles of ionic species emerging from very low dispersion valves. The detector worked pretty well and now we would like to use it as a chromatographic detector for RP-HPLC but most of the species we would like to look at are not conductive. My question is this: Does anyone have any experience or reference for indirect conductivity detection with RP-HPLC? Any info directly conducive to a solution would be helpful.

Have you considered negative peak detection?
include a conductive element into your eluent and see if your analyte will "push" it out of the way and form a trough on chromatogram. Reversing the leads from the detector will turn it into a peak.
We use a similar idea for UV/Vis.
Hope that helps