You should also realize that over the years these bodies have been torqued as unibody cars and are prone to distortion.

Take some measurements within the body to see if it's the body or panels. Alot of panels need massaging. Depending on the manufacturer, dies, number of pans made, proper fit will decrease over time and age.

Have you bolted in solid cross braces? (doors removed) These keep the body from flexing for proper rocker panel and pan replacement.