Can you post a few pictures of the problem areas?
Front clip alignment involves adjusting the cab mounts and the core support mount. You might need to raise the front of the cab or remove shims from the core support to tighten the lower side panel of the hood.
Did you have any body work done on the fenders? If so they could have been stretched making the lower gaps bigger. Is the cab pushed to far back on it's mounts?
Mike B
