...but the cams WERE lined up. It's the crank that wasn't. It will need to be re-timed, and I'd run a compression check just to be safe. The purpose of the timing belt covers is to prevent foreign objects from entering into the timing assembly and messing with critical components. OP, is this on a manual or auto tranny? If manual, you will need a timing belt guide for the crank pulley, set at ~ .020".