Shortdog, not only was what that dealership did underhanded, it was probably illegal as well. Nowhere in the warranty does it say they can throw used parts from a different model motorcycle on your bike. The MoCo, like all other companies, can use refurbished/remanufactured parts for warranty repairs as long as they disclose what they're doing, but they can't walk over to the used parts bin and grab something. BTW, the head was most likely from a Touring model, and the two holes are for the front mount stabilizer.
Anyone can make a mistake, so the fact that they botched the guide replacement wouldn't necessarily cause me to go ballistic. But trying to cover up their screwup by pulling the wool over your eyes is something I personally could never forgive. I agree with the others who have posted so far, this guy isn't your friend if he would consider doing something like this. On the other hand, if you can forgive and forget I guess it's none of my business.
Jerry