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Those of you who may own a Fatboy, you may encounter a starting problem. Recently my 2005 Fatboy failed to start. It was serviced and winterized in November of 2012, but in Febuary I decided to run it, as the snow finnally melted in my driveway. It turned over but wouldn't fire. Several Harley Dealerships were contacted and several suggestions were made. I told them how the bike was readied for winter. New fresh gas with Stabilizer. They told me that the early Fatboys had a valve seal problem and my plugs may be fouled, so new plugs were put in, didn't work. Next they said my battery may be getting drained, check and cleaned all connections, still nothing. I actually went as far as buying a new battery, installing and nothing, again! Once, again they said to check the gas line connection to the tank, did that with no response. The shop supervisor at one shop asked if I had a power commander, I said yes, he said to unplug it and bypass the controller, I tried but I could remove the entire unit.
Finnally, I sent the bike off to the shop, after several hours they said my Power Commander wasn't functioning properly, so I replace it with a Screaming Eagle Supertuner and had it Dynoo Tuned. What a big difference in proformance. I gained 13 horsepower and 12.5 foot-pounds of torque. The bike starts quicker, rides smoother, shifts better and has power to burn.
This posting may help you troubleshoot your ride, GOOD LUCK!