If i haven't had trouble becoming pregnant and i take clomid (clomiphene) for a couple of days and then stop, will this upset my cycle?

Not much: It could lengthen out your menstrual cycle by a few days but otherwise it should have no significant effect. So instead of a 28 day cycle you might have a 30 day cycle. Clomid (clomiphene) produces greater follicle stimulation and in turn greater progesterone production when you ovulate. The more progesterone you produce, the longer the second half (luteal phase) of the cycle.