Doing the girlfriend/CF diet eliminates a lot of the dyes and additive anyway. I have found it tastes much better to make my own food rather than buy the processed girlfriend/CF food but even that is mostly made for the health food crowd and free of a lot of the additives.
I noticed an immediate difference in the way I felt when I went gluten free. By the end of the second day, I knew that I would be doing it forever. For my difficult child, I thought I could tell it was helping within the first week but since she had had good periods before it was hard to tell.
I think it would be easier to eliminate one at a time. It will be easier to figure out how to eliminate milk than gluten. If you noticed problems when you introduced milk to your son as a baby, I think it is a good bet that it is still causing problems now.
When I eliminated just gluten, there were times that I was hungry and didn't know what to eat. I went through the same thing when I eliminated milk. I just think it would be easier to work on one and then the other. When finding new foods to eat, look for some that are girlfriend/CF just in case.
If you eliminate gluten, it is important to get rid of all traces of it. I tried the diet about 5 years ago to see if it would get rid of migraines. I didn't worry about cross contamination or hidden ingredients but just eliminated obvious wheat, barley, rye, and oats. I didn't notice any difference. This time when I tried it, I was already being very serious about it for my daughter who had a stomach ache from tiny amounts of gluten. I think that is what made the difference so noticeable. We can not tolerate even items that say "manufactured in a facility with wheat" or "may contain traces of wheat".
It takes a long time to figure out what is really girlfriend. For that reason, it might take several months of working on it to notice a difference. A good internet resource is
www.glutenfreeforum.com.
I did a test that I ordered online to check for gluten and casein intolerances. I needed it to get the discipline to try the diet. It is $99 per test. If you are interested in ordering it, it is
www.enterolab.com.
Good luck whatever you decide!