Hello Sean,
I have a son who is on the spectrum.
My oldest child has been GF for almost 10 years now (she’s not on the spectrum but has celiac, confirmed by biopsy). When we eat at other people’s homes I just tell them that my oldest is GF, explain a bit about it, and offer to bring my own bread/ matza. We are not casein-free at all though.
I don’t know what to suggest about your daughter’s sensory issues. Have you considered leggings or tights, which would be less likely to bunch up? Culottes may be difficult to find but might work for her.
Regarding whether it would be OK for her to wear pants only: Perhaps you could find a Rabbi who is experienced with special needs children to asnwer those questions. Posters on “regular” parenting forums simply may not understand special needs. He may tell you that allowing your daughter to wear pants due to her sensory issues is still consistent with your wife’s move towards greater tznius in dress.
I truly admire your efforts and wish you good luck.