what the pain/bloating could be, but yes its OK to be on estrace for so long - your body doesnt know what CD you are on, because you are still doing estrogen only.
During a natural cycle - the body begins producing estrogen to build the lining the a few days after you begin shedding the previous one. After ovulation, the corpus luteum cyst begins producing progesterone, this keeps the lining in place - if something implants, the HCG keeps the corpus luteum active, producing progesterone, if no implantation occurs, the corpus luteum dies off, progesterone drops, and you shed the lining.
The hormone replacement we are on for DE cycles tries to mimic the way our body would normally work - estrogen to build lining to the triple stripe, then progesterone to convert and hold the lining (usually about 5 days before transfer - roughly the same time it takes an egg/embryo to travel down the tubes naturally after ovulation) - then continued estrogen and progesterone to keep everything in place until the pregnancy test.
Hope this helps and that you feel better soon!
" Some people built castles in the air. She constructed hers from mashed potatoes, which kept down demolition costs." Sarah Sloane, Borrowing Priviledges