Alot going on there, but there are some pretty crafty guys here who may have an angle of attack for you. IF your system worked entirely perfectly at at least one point in time, then could be a simple matter of a burnout somewhere. In the old days there were issues with not using the correct resistors and such.
One thing you sure should do is add a good deal more detail and background on the overall configuration - componentry, brand names, age, routing, in order to help responders make worthwhile suggestions.
\'96SS SOB: SSRI, Herter Tune, Tri-Y II, , 3000 Edge, F/HO bars, METCO extendeds with CV MMC, Bilsteins, currently Vredestein Ultrac Sessanta (315/35 rear)
\'96FWB BUW-Butt Ugly White: PCMPerformance tune, HDFA w/ swissed filter, 1/2 SLP s.s. catback with H- and Flow Super 50s, oem opti rebuilt 3 times, SS Bars, METCO LCA, Airlift 1000, Monroe SS, PowerTrax No-Slip, CTS wheels with +1 rubber. Finally, wait for it... LT-4 knock module!