First thing I would like to say is cool car. I wouldn't ditch the chrome if it is an original SS. But if you are determined, the best way to fill the holes is to MIG weld them closed. Filling them with lead will work but not without being experinced. Most body filler won't last and the holes tend to show after awhile. Plus the filler will have moisture passing through it from the back side of the metal later creating problems with rust. If you are still determined to fill the holes please get a qualified body tech. (someone that has welded sheetmetal) to do the job and hopefully they won't warp the metal.
Let me know if I can help, Good luck.