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I would think your temperatureTemperature measurement might go a bit higher, because your progesterone should increase with more than one egg...but I'm not 100% sure.
Cysts do not cause implantation issues(I checked with my Dr :) ) and only if the cysts are big..(like 70 mm ) or something can they cause oain. Othet than that... clomid cysts go away by themsleves most of the times. I had 2 22 mm cysts in my ovaries on CD3 of this cycle and they were gone by Cd 12...
:-)
Good luck to u :)