Update 2
Thank you guys very much for the information. I just spoke with the shop and here is the deal. They say that they think the check engine light is coming on because the butterflies have been removed and the actuator is trying to close them, but they aren't there. They said that the other Carpenter Rocket they work on does the same thing.
Now, there are plenty of guys on here with the Carpenter Rockets and I have not heard about this being an issue for them. I tend to think that they don't really know and are saving face with this, BUT when I asked what they were going to charge me, they said it would be an hour diagnostic and that would be it. I don't think I can complain too much about that.
I asked if they are giving the bike a clean bill of health and they said yes, it runs great. I will pick it up in a couple of hours.
Of course, the check engine light is still on...
I would like to get that taken care of, so I am open to any suggestions that you guys have, keeping in mind that I don't know my arse from a hole in the ground when it comes to mechanics!
But my brother is pretty good and he recommends another guy if need be.
I am going to pull down tune ECU and get the cable, so hopefully I can be some use.
Thanks again guys, I really appreciate your information!