Electric Fan Conversion

[touretteboy]

Hello all.  I installed a set of electric fans in my 2001 Silverado 3500, 6.0.  Install went as planned, pinned everything correctly, and had the PCM tuned.  Everything works, however, my battery indicator constantly flashes on and off.  I positioned the positive wire from the fan harness to the back of the alternator (as instructed), and the negative cable to the negative battery post (as instructed).  I do have a two battery setup, with the negative cable from the second battery attached to the first battery (where the negative cable from the fan harness is hooked up to).   I upgraded the alternator to a 135 amp when I went to the two battery setup to accommodate the upgraded audio system.   The truck runs fine, it's the flashing battery light that concerns me.   The service engine light is also on, but that is most likely as a result of a crankshaft variance relearn procedure to be needed (from the PCM tune).  I did a scan with a basic OBD scanner and the truck's throwing a P0405 code (EGR), which I don't think would cause the battery light to flash.  Do I need to reposition the positive and negative cables from the fan harness?  Upgrade my alternator again to a higher amp?  Thanks for any advice.