Hi - Crohn's symptoms (diarrhea, weight loss, pain, malnutrition etc) can present differently in different people. When I was first diagnosed 40 yrs ago, I had no pain, so my doctors did not think of Crohn's - and diagnostic techniques then were fairly primitive, with no colonoscopies or endoscopies. I remember being one of the first patients in England to have the Schilling test (test for B12 absorption), but this is only an indicator, not a definitive diagnosis. When I finally had pain in the lower right quadrant, I had to have a laparotomy to enable a diagnosis.
In the last few years, other non-invasive tests such as a calprotectin assay stool test and C-reactive protein blood tests, which, if elevated about the norm, are a specific indicator of inflammation somewhere in the body. This in turn will help the gastro decide whether to do invasive scope tests, with biopsies.
As far as side effects to meds go, I was very surprised recently that after a Remicade infusion and methotrexate injection the day after, I suffered a severe reaction, (purple spots, difficulty in breathing, pain right up my spine) so my gastro discontinued the mtx. I had been on it for 9 years, so it seemed improbable this was the cause. However, after 4 weeks of discontinuing the mtx, but still on 8 weekly infusions of Remicade, I am better now than I have been for years. I can't speak of Humira side effects, as I have not had this immuno-suppressant...yet! Most drugs can cause allergic/intolerance reactions - in some people, but not all. For instance I only had two doses of Azathioprine, but within 24 hrs had to call a GP out to my home as I had severe vomiting and diarrhea and rash all over my body. He advised me to stop the drug immediately and that is when I started on mtx. I guess over the years, I have become intolerant to it.
Crohn's is an insidious disease, and even experienced, competent gastros are sometimes perplexed as to how to deal with a flare. I have found it is a case of trial and error with different drugs, and then be aware when things are going wrong.
Hope your son soon gets some answers.