Yes, it will... Persoanlly, I wouldn't run Clomid until I was FINISHED with my cycle. Even thogh EQ is milder then some other AAS, you would still be running Clomid DURING a cycle and not post-cycle as a recovery agent. What is your current cycle btw?
Follow TheRide's advice. Don't run any gear while you're running your pct. You should wait at least 2 weeks after your last shot of EQ before doing your pct.