Bethany,
I am currently ttc #2 also. I have been seeing a RE since April. I was pretty much in the same boat as you...no period since the birth of my 3 yr old. I also exercise a lot and was told to cut down on my exercising and gain a couple of lbs. My RE put me on estrogen for 3 weeks and then I took medicine to get a period. Once I got my period, we started with injectable meds to make my folicles grow. I went in 2-3 times for vag. ultrasounds to monitor their growth. Once large enough, I give myself a trigger shot in order to ovulate. I am doing this along with IUI.
I have just gone through my 2nd IUI (the first ended in an early miscarriage). My periods are now regular.
What I am trying to say is maybe your body just needs kick-start (like I had) to get your body working correctly.
HTH!
Judy