Bella, Had to reply to you as i have been through almost exact same thing.
After 2 m/c's on clomid, i was changed to puregon/IUI. My first cylcle went like clockwork and resulted in my DS. Late last yr, we decided to try for no#2. Did exact same cycle dose etc but was a total disaster. First did not respond well to puregon so dose increased. then got 6 mature follies but E2 was very low (same as you). Cycle was cancelled although i was told to trigger just to release eggs. We DTD anyway but no chance of pg with E2 that low.
Very low E2 can mean there is not enough natural LH in your body. FSH ( puregon ) stimulates the follicles to develop but reasonable levels of natural LH are required to stimulate the follicle lining cells to produce oestrogen. The good news is, all it took was the addition of low dose pregnyl (100iu) every second day. Pregnyl is used to replicate the LH surge at high doses, but at low doses will act just to help produce E2.
My subsquent cycles (sadly, there has been many!) have all had good oestrogen levels with the pregnyl. Only bad news is that you'll have more injections to give.
Hope your situation is the same and this works for you too!