You have a pro trainer, so I do not feel appropriate to give advices, but can share my own experiences.

I had a somehow similar problem. For me the help came from Pilates BOOKS. Books have more time, space for narratives than classes, videos. Because I am much more interested in the healing effect of Pilates than the "inch loss" effect, these books seemed to me much better sources.

They all recommend the same thing: first doing separate neck stretching exercises, then as a second step modified versions of the Pilates exercises, and ONLY when you can do all this to do the original version of the exercises. Simply by doing the same hard exercises involving your neck again and again your neck would not "get used to it." They all advice against continuing an exercise when your neck in pain.
Using this slow approach after 4 months I could do even the advanced exercises in the original version, without any neck pain.

But this is only my $0.02