The counts per inch will be related to how many revolutions your encoders make while the screws turn enough times to cause an inch of table travel. If you have 1000 line encoders, the galil interprets those as being 4000 counts per revolution, since it can discern the leading and trailing edge of each positive and negative encoder pulse.
So if your screws are 5 theads per inch, then the encoder pulses per inch would be 20,000. Any error in the calculation should be very noticable, as it will likely be something like 25% or 33% or 50% off.
Your cbk file is a backup or storage file of all your settings. It is not actually used while the gui is running, because the cbk is a compilation of many files.
The settings for your limit switches are in the card.ini file. I forget which directory that file is in, but you can look for it. However, I think before you edit that file directly, that you should be able to make all those settings while in setup mode, not actually running the controller.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)