About to do IVF, have Factor V Lieden and on BC with sever migraines - very worried!

I am 41 years old and since the birth of my 20 month old son (via IVF) I have had Migraines starting at first a couple of times a quarter to once a month to now once or twice a week. I am about to do another cycle of IVF to try for a sibling for my son before it is too late and was put on birth control pills (instead of Lupron which is what I took before for IVF). I took the pill for several days starting the 2nd day of my period and then stopped becuase they changed my IVF schedule. 3  days later my bleeding was so severe and I had such a severe migraine I ended up in the emergency room. They checked my blood work and everything looked normal and they also gave me a cat scan. The IVF dr gave me 4 vivelle (Estragen) patches to wear to stop the bleeding. I have a blood disorder called Factor Five Lieden (hetrozygous)  and because of this I am also taking daily shots of .40 ml Lovenox. They re-scheduled my IVF and put me back on the BC and blood thinner. I have been back on it for 14 days and have felt sick to my stomach, tired and have suffered at least 2 severe migraines. I have been told to continue with the BC until July 22nd at which time they will put me on stumulating drugs (follistim) to start the IVF but I am worried about the migraines and how I have been feeling. Is all this safe? I do not have any aura with my migraines - just terrible dull pain on one side that usually moves across to the other and then severe nausea (never thrown up though!) and it doesn't seem as though I am sensitive to light or noise much.