I am on my second cycle of Clomid (100mg). The first time around, the side effects didn't really kick in until a few days after I started taking the pill. I took it CD3-7 and the side effects came on suddenly on CD6. I've heard some don't feel the side effects until a couple of days after they take the last pill.
My side effects were mainly a headache and upset stomach. I also got a few mini hot flashes at night. Then around CD9, the side effects went away.
Hopefully you won't have any major side effects though.