Someone PM'd me about this thread, so I thought I would post an update in case anyone else stumbles across it in the future.
After my post in 2009, I cut way back on my training and purposefully gained weight (my doctor called it the "ice cream diet"). With those modifications, my cycles started to come back, though they were very long. With the help of clomid, I conceived my daughter in August 2010, and I now have an almost-three year old!
After I had her, I switched my focus to running, and actually lost a fair bit of weight (lower than when I was first posting). But, the combination of lower overall training volume and hormonal/weight switches after pregnancy were enough for me to get pregnant on my own this time, and I'm 5 months pregnant with a baby boy (and still running every day!).
A couple of great resources for people trying to get pregnant while dealing with these issues: http://noperiodbaby.blogspot.ca/
- great blog with lots of links and info, plus personal experiences
And there's a hypothalamic amenorrhea group on the Fertile Thoughts message board that is worth checking out.