Hello.
If I understood correctly the drills you make change only in sizes. If that is correct the system I´m about to describe might be a good solution. If for any reason you need to enlarge a hole by moving the tool in a path around a given position, that would not be possible and you would need a full CNC system.
Trajectory generation as that performed in let me call them standard CNC machines requires a lot of mathematical computations for the tool to move along a mathematically defined path and kept close enough to it so that deviations are kept to a minimum.
In your particular case it does not matter how the tool is moved from one point to the next. At this point it is interesting to know that straight lines while being the shortest distance they do not make the distance in the shortest time. What I mean with that is that in this case it is better to let the motor on each axis to move freely unrelated one to the other. That way it may be possible that one motor gets to a target position before the other.
Having said that I would use a simple GWBASIC program to control de positioning of the tool and execute the drilling movement.
One problem I cannot solve "on the fly" is how to automate the tool changing process but since you automate the most of the process manual tool change at a HOME position may not be a problem. If it is let me know.
There might be options using PLCs but to my taste they become expensive and difficult to maintain. In the PC you can set the microstep (the minimum distance an axis moves for a single input pulse) and then have the program calculate the needed microsteps required to move from one position to the next, In low cost PLCs you have to calculate those quantities yourself and feed them into every single move. You can also have the PC repeat the aforementioned movements as many times as you may require as blocks.
Perhaps the newer PLCs allow for block repetitions. I don´t know. It´s been quit a while since I used a commercial one and might not be aware of the advances. The only thing I´m sure of, in my personal opinion, is that their pricing appear to be at least in the range of low cost PCs but without their advantages.
There are a number of "PLC controlled CNCs" that you can watch in Youtube. If you do, notice that they normilly move in straight lines either horizontal, vertical or 45 degrees. That is because they don´t really sincronize the motors.
If you would like to know more about this idea please let me know.
Regards.