With the ignition on, but not running, I would check the fuel system pressure at the valve on the right injector housing. Then I think the next thing I would try would be to hook up the S&S software and check things like the temperature sensor and crank position sensor values to see if they make sense. Then basically work through the fuel/spark/compression variables until you find the issue. Intermittent issues are always the hardest to diagnose. Sorry to not be more help.
