Thanks Jeff so I can weld them all up?
Using your original post as a guide from top to bottom
1- Drivers side fender forward. Non-original holes - weld them up and finish
2- Drivers side fender rearward = Appears that someone changed the fender and redrilled the rocker molding forward hole but not the two smaller ones for the plastic retaining clip. Are the moldings going back on the car?
3-Yes - non factory so weld them up
4- Appears in the other pictures you posted the passenger fender forward lower edge also has the same holes as #1 above so fill those also