The headaches and nausea might be from the LDN as his immune system adjusts. If I was in his position I would give it a month, or better, two months. The body takes time to adjust. If he decides to stop taking it then he should also watch for the recurrence of subtle symptoms that LDN may have helped with but that he didn't notice had disappeared.
4.5 mg isn't an ideal dose for everyone. I can't tolerate more than 2.5 mg, some can't tolerate more than 0.1 mg, while others go up to 9 mg. It takes some experimentation to find the dose that does the most good for a long period of time.
Your son may also unintentionally be doing (or experiencing) things that interfere with the effectiveness of the LDN. ie. Dairy and gluten can both interfere.
This site lists many things that can undermine the effectiveness of LDN.