b20vtechatch

i just did a rebuild on my b18a1. I used a gsr water pump and gsr timing belt. Now i cant get my cam gear sprokets to line up straight. the arrows pointing up and the two lines arent lining up. has anyone had this problem. they are off just a little. i started the motor and its running rough. i timed it and its still running rough. is it because the spokets arent line up perfect. how do i get them perfect?