You can use NPC several different ways:
1)from cd 14 to 28 or ovulation to menses. This allows both ovulation and menstruation.
2)from cd 7 to 28, like you would take the pill. This blocks ovulation, but still allows a bleed (not technically menstruation since there was no ovulation)
3)consistently for several months (up to 6 mo's straight) to block both ovulation and menstruation and give the ovaries a break.
The NPC package will have dosage amounts, but I usually use 1/2 tsp in both Am and Pm, rubbed onto face, upper arms, belly, thighs, neck as long as you rotate where you apply it each time. I second Amber2's recommendations for Dr. Lee's book.
I've heard good things about using acupuncture. My cousin used it to lengthen her short cycles. I keep thinking I'll try it, but never seem to have the money when I have the time and vice versa. Let us know how it works out for you if you try it!
I thought your correlation between the cysts on your face and on your ovaries was pretty good. In my opinion, they're both ways the body is trying to trap, then release toxins. Our bodies are just getting stuck when it comes to the "releasing" part and we have to help it along.
Also, nice to meet another vegan!

I'm just starting back eating that way after being away from it for a couple years, so I consider myself "almost vegan" but not quite all the way yet (98% maybe). If I remember correctly Dr. Lee briefly mentions in his books about how animal and soy foods can interact with hormones, so by not consuming them you are already one step ahead of the game!
Best of luck to you!