It's possible you could have a luteal phase defect even with high progesterone at day 6, if the corpus luteum doesn't last long enough. But luteal phase defect means a decreased time (less than 10 days) between ovulation and menstruation, and from your post it doesn't sound like that's your problem.
Estrogen helps build the endometrium during the first two weeks of the cycle. Clomid is an estrogen receptor blocker, so can cause thinning of the lining - especially at high doses. Your RE could prescribe supplemental estrogen to help build the lining further (and increase fertile cervical mucus), or you could try taking something naturally estrogenic like evening primrose oil (EPO, available where supplements are sold) during the first two weeks of your cycle.
Hope that helps! Good luck with Clomid - this cycle made me crazy too.
