If your Harley-Davidson Shovelhead's flywheels appear to be running in the opposite direction as indicated in the factory service manual (FSM), but the bike runs well without any noticeable issues, there could be a couple of possible explanations:
Timing Mark Misalignment: It's possible that the timing marks on the flywheels or the timing hole are misaligned or not accurately indicating the direction of rotation. This can occur due to manufacturing variations, aftermarket modifications, or other factors. In such cases, it's essential to rely on the actual performance and operation of the motorcycle rather than solely relying on the visual reference of the timing marks.
Reversed Primary Drive or Transmission: Another possibility is that the primary drive or transmission components have been modified or reversed, which could affect the apparent direction of the flywheel rotation as seen through the timing hole. In some cases, owners might have intentionally made modifications to the primary drive or transmission, resulting in the reversal of the apparent rotation direction.
It's important to note that Shovelhead engines were manufactured from 1966 to 1984, and over the years, modifications, repairs, and customization work may have been performed by previous owners. As a result, deviations from the factory specifications are possible.
Given that your motorcycle runs well and doesn't exhibit any issues, it suggests that the engine is functioning correctly despite the apparent deviation in flywheel rotation direction. However, it's recommended to consult with an experienced Harley-Davidson technician or mechanic who is familiar with Shovelhead engines to inspect your specific bike and provide a more accurate assessment based on a physical inspection. They will be able to provide more specific insights based on their expertise and may identify any modifications or factors that contribute to the observed behavior.