My physical therapist says he's putting me in the "proper alignment" and now i am having difficulty walking. advice?

Huh?: What was malaligned that needed re-alignment? Is the difficulty in walking secondary to pain? Physical rehabilitation often takes time and efforts both from the patient and the treating therapists, if you are uncomfortable or deteriorating from treatment, isolate, with detail, your primary complaint and immediately address your therapist with your concerns.

See an osteopath: Don't mean to sound harsh, but have heard this before, and physical therapists are not trained to be chiropractors. Visit an osteopathic physician, get full history and physical exam, and find an appropriate program for your issues.