Again, thanks for your thoughts!
Jim, good idea, but sadly not possible. The way I state above is the way it has to be done. I do projects of adapting various different slr lenses to fit different mounts, this involves using some standard parts/mounts that i cannot machine myself. But thank you for the suggestion.
Dave, the M3 counterbore I was looking at is
this one. From the description, I'm thinking the 'max diameter' (ie where it cuts) is the M3 size??
I don't actually have such parts available to photograph at the moment. They come up frequently, but not right this minute

, hence the (poor!) diagram. Will try and get something soon though.
I've been thinking more about how to mount/hold the piece that needs drilling. These are generally small rings or tubes made of soft metals (aluminium, brass) and need drilling at 4 to 8 points around the ring (this is most common, atleast). I'm thinking a vise of some sort would probably be a good investment and would make the job quicker/easier/more efficient (rather than building something myself that might not work for every piece). I'm unsure as to whether to get a rotary table with a 80mm chuck in (like my lathe). As the rings are made of soft metal, perhaps this would not be ideal, as I generally can't grip them too hard without distorting them (no problem on a lathe I've found). But perhaps with the downwards pressure of a drill, it might not be good enough. (
eg: like this)
So perhaps a swivel vice of sorts would be a better option? The problem then is the grip is even more uneven. The rings are sometimes threaded, so if i could make a tube of sorts that could first go into the vice the ring could just be held in place, and then moved around with ease. Really not sure.
I cleaned everything out today and put the big thing on a better surface. I will take some photos later so you get an idea of the monster I'm working with ;)