Alright, what you need to do is 'hook up' your limit switch signal to the homing signal pin in HAL. If you look in the hal (and familiarize yourself with the format) you can see that 'both-y' is connected to 'parport.0.pin-11-in', creating a new pin (both-y) that is used for both your Y axis limit switches. If you scroll down in the HAL file to the Y axis portion, which can be found by looking for all the parameters and pins with 1s in them (0 is X, 1 is Y, 2 is Z, etc)(stepgen.1.maxaccel is the max acceleration that the step generator 1 will use, for instance). You can see that the pin 'both-y' is connected to both 'axis.1.neg-lim-sw-in' and 'axis.1.pos-lim-sw-in'. This tells LinuxCNC that when the parallel port pin 11 is active, either the negative or positive limit switch is reached. To also set the limit switches as home switches, you simply connect the same signal to the respective home switch pin in HAL. To do this add this line at the end of the Y axis block:

net both-y => axis.1.home-sw-in

This needs to be done for each axis, except with 'both-y' changed to 'both-x' and 'both-z' in their respective places and 'axis.0.home-sw-in' for x and 'axis.2.home-sw-in' for z. If you aren't a perfectionist you can just add these three lines to the end of the HAL file.

Now to the .ini file. What you need to do here is tell LinuxCNC that your home and limit switches share a common switch and signal as well as set you axis limits and homing speed/direction. I'll use the X axis for example, but it needs to be done 3 times for each axis.

To tell it that you are sharing home and limit switches, simply add 'HOME_IGNORE_LIMITS = YES' to the [AXIS_0] section. Do this for all axes.

Now you can set 'HOME_SEARCH_VEL' and 'HOME_LATCH_VEL' and 'HOME_FINAL_VEL' to the velocities you want the machine to move in each stage of homing. See: Homing Configuration for a good explanation. Do this for all axes.

I'd then set 'HOME' and 'HOME_OFFSET'. They are described in the above document just as well as I can describe them. Do this for all axes.

Finally, set your 'MIN_LIMIT' and 'MAX_LIMIT' for each axis. These may change a bit depending on your 'HOME' and 'HOME_OFFSET' values. Do this for all axes.

I found it easiest just to kind of guess and check to set the HOME, HOME_OFFSET, and LIMIT values, although I'm sure the sign conventions make sense. I just adjusted the signs and positions till the pattern and distances made sense. You can also set 'HOME_SEQUENCE' if you want the Z to home before X and Y, or any other combination.

Hope this helps. I'd back your files up first, just in case. You can do this one step at a time, that way if something doesn't work you'll only have a couple steps to check. Once you skim the HAL manual and Integrators manual and do this once it becomes quite easy and extremely configurable.