man, i know exactly where your coming from. i had the same problem of only using the index finger all the time, but i suffered from lack of strength. When i bought my YZF, i made a concious effort to use two finger all the time, and it worked for a while but i kept slipping back into the one finger routine.
i got hurt and left the MX track for a while. I stayed with riding on trails, and stayed with the two fingers again. it was easy because there was no stutters or jumps to worry about. I must have ridden those trails for about a month before heading back to the MX track. Went for a lap and looked down at the bars. Two fingers! even on the stutters and jumps, they didn't move off the leaver once.
so i guess its just practice, and more practice.