It is tricky and so individual. Many people's reactions are triggered by natural substances, dust, dust mites, mould, pollens, animals etc and some by chemical substances.
DS2 is sensitive to anything petroleum based, polyester, latex, rubber but OK a with wool, cotton and horse hair. Many of the anti allergy fabrics don't work for him and when the futon company started adding natural latex into their mattresses I might have actually cried.
You will find what it is!!
The suggestion of trying the top bunk is a good one, the air flow may be better. DS sleeps better a ground level without a bunk above him and sleeps better on a wooden bed rather than a metal one. I have given up trying to work out why, but simply grateful we get sleep and he is better. I would also consider removing your older daughter, perhaps at the weekend, to see if that makes a difference.
We also use blue tansy essential oil diluted and rubbed in his chest, feet and hands. He reacts really badly to ventolin and salbutamol so will do anything to avoid him coughing and wheezing. (I stop short of chanting and dancing round his bed to clear the chi!)