Homebrew PCBs

Just finished my first toner transfer board which has made me think 
maybe a CNC routed board would be better. Am retired on a minimum 
budget so like free software:

Saw a lot of people use Eagle, but afterlooking at the Eagle website 
wondered if the free version is only good for making one board or did 
I misread? With my learning curve it would take 10-20 attempts to get 
my first board.

The PCB's I am interested in making at present are predrawn in a PDF 
file for toner transfer. Is it possible to modify these for milling?

After I get a drawing in the right format for milling, what program is 
used to generate G code etc.? At present am using A9CAD to make 
drawing, ACE to convert to g code, then Mach3 to control my router.