It sounds like a module problem. Go to the top of the page and click on manuals under the support tab. The heavy maintenance manual goes into detail on how to troubleshoot the ignition system in the electrical section.
So I put new plugs in and disconnected the SS and problem continues, rough running on one side. I suspect it's the top module. I'm going to see if I can find one somewhere and switch one out to see if that corrects the problem.
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