Has anybody any experience of or recommendations for a drill format converter, preferably Linux based?
Have you seen the Skeinforce tool chain they use with the reprap.
http://reprap.org/bin/view/Main/Skeinforge
It is written in python and you might be able to patch together some elements of it to just get your drilling data out of it.
Thanks, I hadn't seen this, although I do look in on the reprap people now & again. They certainly keep busy.