What's the best way to repair these holes

Back in the early 70's, I had a car with the same problem. I took it to an old guy that did leadwork. He ground it all down, leaded all the holes, and repainted it. I had the car for at least another 5 years after I got it repainted, and no rust ever showed up there again.

I dont know how long it really would have lasted, however, and I dont know if they still allow leading, or if anyone still does it.