I m a tunnel engineer and I think, that your problem is really interesting. You probably need a basic method first, how to execute that work and how to observe and control the results.
In my opinion there are two options.
- to program relatively simple program, which takes tunnel axis and tunnel chainage as a base and measure distance from it to set the right location; the tunnel final lining positions, niches positions and other thinks in tunnel are set this way. I think the best way is to program something in lisp or visual basic as an add in Autocad.
-I visited the other day a company here in Slovenia, where I worked years ago. A the moment they set a platform for tunnel design, which consists from real 3D model of a tunnel, including all niches, tunnel excavation phases and other things. That kind of model may be useful for your purposes, too ( to set the position of the holes within the model, which of cours, must be created first).
I did some programing in past, but I m far from being a proffesional and I m unable to done this job. But if you are interesting, I can give you a contact with those boys.
best regards
J