Do infidel thoughts associated with a non-infidel act of disobedience, or the feeling of prostrating to other than Allah during prayer, or the mind wandering to infidel matters during acts of worship, change the original intention of the act, knowing that this may be an obsessive-compulsive disorder?

What you experience of waswas (whispers of Satan/obsessive thoughts) you are not held accountable for. Rather, you are held accountable for your intention. So long as you intend to prostrate to Allah, you are rewarded. The cure for these waswas is to disregard them. As for your committing sins, you are held accountable for your actions, not for the accompanying waswas.