I don't have Chron's but UC, er, did (had my colon removed ~3yrs ago. Anyway, autoimmune disorders run in my family (sister and I have UC, mom and aunt RA).
Anywhos, I know UC and Chron's are different, but they do share a good bit in common. In all honesty, I think the best thing you could do would be to keep a food/symptom diary. Track what you eat and what symptoms you experience. This will help you to determine what can be causing flare ups. Also, sometimes people like to do elimination diets (like cutting out dairy and red meat, etc) and then after a while, add them back in bit by bit - if it worsens symptoms then you know that may be a flare-causing food. Some common no-no's are corn (I never had issues with it though), popcorn, nuts, and in a flare, anything raw (veggies/fruits). I typically avoided apples and things that were really "rough" but if you baked them or something, I think that would be okay. My sister can't eat too many slices of peaches because they cause her to have issues. She used to struggle with spicy foods causing pain but that seems to have improved over the years.
So really, it is a personal response sort of thing which is frustrating but it's just the nature of the beast.
To help with weight, if you are having problems in a flare, I would suggest eating whatever you can handle. I used to have to make high-cal milkshakes that my GI recommended. There's this stuff called Scandishake that you can buy online. It's little packets that you mix with 1 cup of milk and it automatically gives you like 500+ calories. I won't say they are super nutritious, but they do have calories! Also, nut butters (not crunchy!) may help. If your body isn't absorbing calories properly though, I'm not sure how much these things will help. I know I lost lots of weight at various times during serious flares (although I also struggled with an ED at the time so that didn't help matters any). However, I always managed to get the weight back up in time.
I'm sorry to hear about your diagnoses, but I hope you are able to find ways to keep it under control. Hopefully others with Chrons will be able to help you out. Also, you might want to google the "Chron's and Colitis foundation" as they should have lots of info that could help.
The side effects of allergy medications keep some people from using them. Natural remedies can be a great alternative, but some are more effective than others.