Perhaps you could use karel code to read the values from your measurement machine. Read them in tranches of 100 at a time, say.
So, your program calls READ1-100.PC, which will be some karel code to read the first 100 values into PR[1] to PR[100].
Then drill your first 100 holes using PR[1] to PR[100]
Then call READ100-199.PC, which will now overwrite PR[1] to PR[100]...
now drill your next 100 holes...
... and so on until they're all done. Does that help?