Although I have no direct experience with pilates, I think it is a higher level program that may or may not solve your problems directly. I feel you have significant postural and muscular imbalances that need to be solved first. Yes, it appears that your muscle recruitment patterns are altered, this is the bodies way of protecting itself, however it is now time to solve this problem.

Without full assessment I couldn't say what your real problem was.

I am a muscle balance and function practitioner, normally in this situation I would provide specific postural and muscular balance program, as I believe based on what you are saying that these are your problems.

Will keep in touch later this week, Regards