I can honestly tell you that I have been where you are and am now on the other side with a beautiful and vibrant daughter who will be 5 in February. At her birth, the dr's noticed that she had no soft spot. Within hours she was diagnosed with a rare genetic disorder that we did not know that I have. She was scheduled for a CT scan at 36 hours old. She eventually had it when she was 3 1/2 days old. For her it was extremely easy. We were at CCMC and they are wonderful--in general, everyone working at a children's hospital is great. They know and appreciate kids (of ALL ages) and interact with both kids and parents appropriately--understanding the impact this is having on the parents, especially. The scan is very easy--our daughter did not need sedation for it because she slept through the entire thing. However, our other daughter has required sedation for other reasons, and all is well there, too. She is angry when she comes out and takes a little while for her to calm down, but otherwise, sedation and anesthesia have gone smoothly for both of our daughters.
Our first daughter had craniosynostosis--the premature fusion of the bones of the skull. Clearly, this is not what is being considered for your son. At 6 months, she underwent surgery to separate those fused areas--like I wrote above... she will be 5 in February and is a beautiful, vibrant, intelligent little girl. It is completely unknown to anyone unless we say something. I tell you this to offer my support and to let you know that you are NOT alone with craniofacial differences. I pray that everything will reveal to be as it should be, but if the scan does show that further tests/action is required, you will be fine. Your baby will be fine.
Please feel free to contact me with any specific concerns or even questions about what we went through. I am comfortable talking about it... now. Both of our children have undergone anesthesia (the first one at 6 months; the second one has been sedated and undergone anesthesia multiple times since she was 2 months old), so I have been there and can hopefully help you to understand what to expect. My prayers are with you and your baby boy--May God be with you tomorrow.