If my cycle is only 3 days long...is it best to take clomid on the third day to conceive?

Not first step.: Your first step would really be to see if your time of ovulation is regular and predictable. Take your first morning temperature with the same thermometer every morning for a few cycles. Your temperature should increase by .5 to 1° at the time of ovulation. If there's regularity here, then you might not need medications for conception.