Ok i was on the phone - i found this wonderful forum thread with a doctor answering the questions, and once it was explained it seemed to just click and make total sense !
So every month every woman has an active number of follicles, and just after CD 3 your brain begins an decrease in FSH production (which is why they do FSH draws on CD 3), and the strongest follicle at that point is the one which will be ovulated.
Now since Clomid causes additional FSH to be produced it works like this - After day 5 the follicles have already experienced the FSH decrease (or starvation, if you will) and the single follicle has already been chosen as the strongest, however is Clomid is given on day 3 then the follicles haven't yet experienced this starvation, and you MAY be able to pluck 2 follicles instead of the single one.
Also research suggests only about 10% of women actually notice a decline in CM while on Clomid, and thusly only about the same percentage would have a thinner endometrial lining. Now im sure this could be argued, and as someone who has a hard time determining most CM to begin with i may have to err on the side of caution and assume i have a thinner lining and CM and adjust with natural supplements accordingly, while this might not hold true for someone who pays close attention to and fully understand their CM. Also its pretty much too late to determine the changes in CM on Clomid if you weren't familiar with them prior to having been on Clomid (which also makes sense)
So we've been told that there's a higher chance of weaker, multiple follicles the earlier days, with stronger singular follicles on the later days, but this may not be totally true, as a slight extension of FSH could still allow for multiple, normal follicles as opposed to weaker ones.
I think it's all kind of up in the air but i found it all to be terribly informative. Also instead of editing my previous post i'll just correct it on this one - you should ovulate 5-9 days after the last pill is taken. Taking OPK's too soon after clomid can result in a false positive, but i'd suggest OPK's the day after the last pill and continue on from there to cover all the bases, and do this with the knowledge you may get a false positive to to continue to test as well as pay attention to temps, CM and CP !