I had the same problem. Since my car is far from stock, I decided to take advantage of the situation for a new look.
I used a punch and hammer to knock though what was left of the screws in the body panel. I then drilled it out and tapped the holes with 1/4x20 threads.
I went to the hardware store and bought some really cool stainless 1/4 x 20 alan head bolts. I then drilled the hole out a tade larger in the rocker panel. I attached the rocker panel with the new bolts for that wicked rough and ready industrial look of the alan head cap screw bolts. It looks awesome and fixed both problems at once.
The tap, bolts, drill, etc. put the whole modification under $30.