Yes, check your engine.
Seriously, you need to obtain a (free) copy of the S&S Protune software (
https://racing.sscycle.com/support/) which requires a Windows computer and a cable with a Mini B end, and plug it into the ECU to see what the error codes might be. There are many possibilities of error codes. If the engine appears to be running fine, there is a good probability it's related to the automatic fueling adjustment made by the ECU going beyond its design threshold. You can (usually) reset the check engine light by disconnecting the battery for a few minutes, but then you won't know what caused the error in the first place. I would get the software and see for certain what the issue might be.
