The easiest proper way to delete the holes is like this...
1, Clean both sides of the hole of ALL paint and any rust.
2, Cut some 1 inch squares of mild steel the same thickness as the door skin, then with a grinder, just put a radius on the square edges (this will help stop rust forming in the future)
3, 2 sets of hands are useful at this point, place a cut plate behind the hole, taking care to position the plate centrally, so as not to weld only the edge.
4, With a helper firmly holding the plate in position, tack weld the plate in place, but with only one tack, heres the important bit! use an airline, and blower to cool the area immediately the weld has been made, this will minimise distortion to virtually nothing...
5, All holes must be welded through 360 degrees, for a perfect platform to finish off with body filler, just tacking the plates on with one or two welds is not sufficient, and will show up in the near future!
6, Finish the welds with a belt sander, with a 60grt belt fitted, make sure not to get the panel too hot
7, When finishing with filler, skim the entire length of the door, rather than filling each area individually
8, Dont forget to Waxoyl the inside of all the panels when done
HTH
Thom