Ok, I'm still struggling with this problem. I have a card that will sample the signal and calculate the duty cycle for me, but I have no idea how to use it, and the guy that does is pretty busy to help me.
When i used the RC filter that nigel suggested, I was getting some significant ripple in the output. I dont know if it was because the signal is only running at 100Hz? I was thinking about maybe using a PIC to read in the 100Hz signal and up it to a higher freq. pwm then to the RC filter. Does this sound like it would work?