I can remember mine having bad rear sites errors. If I remember correctly, it is when the mapping cells go outside the base map for whatever imitating circumstances.. Stock bike no mods except maybe the baffles opened up. Jason ended up having the bike taken to the shitty side of the rainbow where they could kick it over and probe it with no one watching. Said the endo factor was a cut plug wire but replaced the ehc among other items. Throttle bodies have been know to have undersized shafts in them and a intake leak also will play havoc but can be detected through software readings. O2 sensor will cause these issues as well.
Sometimes it can be as easy as reteaching the base map to what it has learned so it can go from there.
What dealership is it at? Where are you at?
Big Dog needs to put a script on the home site and provide EFI owners with a communication cable that they can hook into the ECU and to a laptop and open up BDM site and let it tell them the alarm that is being generated and if it is a nuisance alarm or serious problem.
Most can download the S&S software from the S&S site and look for themselves if they have a little computer savvy. I ought to make the cables for them and send it to those that want them. Maybe I need to just make a care package for all the EFI owners with software and interface cable so they can look up their own alarms and call BDM and tell them what is going on.
Without knowing what is setting the engine light baddog64, it is hard to say what to do. If you know he alarm which instruction are already written on this site on how to access your module and where to download the software from, you are at their mercy.
Sulconst2 has posted a awesome troubleshooting guide if you know the alarm. download this and keep it.
http://www.bigdogbiker.com/forums/efi-topics/3810-flowchart-troubleshooting-chart.html
I hope we can be of assistance here on the forum, but Jason and Dogvet are the experts here. Perhaps thet need to be more open to what is ailing these EFI bikes seeing how they are having to troubleshoot them all. Honestly gets you everywhere in customer service.