Along with the bloodword on CD 6 I would request a vaginal ultrasound to be sure that the follicles are not getting too big...in essence resulting in a cyst. Also if she does ovulate then they need to do an ultrasound to make sure that the follicle collapses(breaks and lets the egg loose). If the follicle doesn't collapse then the result is cysts.
Definitely take the Clomid at night so she sleeps through most of the symptoms. And Clomid is usually taken CD 5-9. What mg did they prescribe her?

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Jaime(31)-DH(41)
9/29-12/10 4 failed IUI's--2 natural, 2 Clomid
2/16-4/13 BCP's
4/7 Begin Lupron
4/23 Begin Gonal F and Menopur
5/3 Egg Retrieval 8:15
5/8 Egg Transfer (2 5day blasts)
5/17 BETA DAY=BFP 241 9dp5dt
5/24 2nd Beta= 9,239 16dp5dt