I have done a few experiments in this direction and generally don’t bother with drill files.
The whole concept of “footprints” hardly exists in the gerber files, and therefore I do not even try to reconstruct it, because it’s very easy to simply use new footprints.
So I just throw away all the re-imported pads, then recreating the schematic and position new footprints over the ends of the existing tracks.
I did a write up about that (which still needs cleanup) and posted it:
The file you list is in Gerber format, and you seem to read it with an Excellon NC format input.
Apart from that, there are some strange lines in the Gerber file, like
04 PROTEUS GERBER X2 FILE
Could it be that you copied it wrong, and it is actually?
G04 PROTEUS GERBER X2 FILE
You could check the file on the Reference Gerber Viewer, that should be able to tell you whether it is valid Gerber or not.
Because Excellon has been used for so long and many manufacturers expect it or at least understand it, and some may not handle Gerber drill files directly.
That’s the basic problem with everything related to Gerber. Even though it is about as good and modern file format than other formats, it has too much historical baggage. Recommendations and best practices can’t be forced for output (EDA software) or input (manufacturers/CAM software), and especially cheap and popular manufacturers use old software and old conventions, and even so that different manufacturers use different conventions. I would like to see even one cheap manufacturer who actually takes modern Gerbers with all recommended and best practices so that everything possible in a design is defined in the Gerber files and nothing else is needed.
It is indeed said that some fabricators do not handle Gerber drill files. However, I wonder if this is still true, or, rather, to what degree it is not true. Thinks slowly, very slowly, improve.
Does one know fabricators that would refuse a job because the drills are in Gerber?