Hey dandy - did your doc tell you to start on CD11?
I don't think it will mess you up... my doc does a scan and bloodwork on day 3 of my cycle before letting me start the clomid. I had a 17mm cyst or follicle, we had to wait for the bloodwork to know if it was a follicle or a cyst. The bloodwork came back saying it was a cyst. My doc said if it was a follicle, that there would be no point to the clomid (not that it would mess me up, just that my body was already doing its own thing and the clomid wouldn't have an effect).
If you have long cycles you might not have had a dominant follicle in which case the clomid will make sure you do have follicles that grow to dominant sizes.
Thats just what my FS told me though.. everyone always seems to have a different opinion on this.