I've had lessons from a professional voice coach, and she basically told me to relax, and make sure my chest is vibrating when I talk. Hold your hand on your sternum, and you can feel the difference between a rich voice and a nasal voice. Basically your upper throat should not be involved, and your breathing should be deep and air propelled out from the stomach. It's sort of like picking a lock, it's something where you have to visualise what your muscles are doing, and where they are at at all times, and be aware of when your throat contracts and goes into nasal mode, so you can avoid that.

Hey man, I don't have PCOS so I can't speak from any experience there, but I've been on T for 6 months.

Pre-t my voice did instinctively go to a higher pitch when I wasn't consciously making an effort to lower it, or when I was excited about whatever I was talking about. Controlling vocal cords and lowering my pitch was definitely made easier by practising several different voice exercises:

http://www.youtube.com/watch?v=MiGvdm7Zo-s

http://www.youtube.com/watch?v=VKuVRfKO5qM

Don't strain your voice, if it hurts when practising, stop. Always stay hydrated. Practice pays off.

I'm not sure if muscle memory applies to vocal cords, advice I've gotten from trans* friends and mates who have experienced speech therapy - speak from your chest, not throat (if you're aiming for a deeper voice). Mentally visualise your voice lowering from your throat to your chest. I didn't get much help from this alone, but I did it anyway while following the videos.