The board you soldered the pins to is a break out board BOB hence the BOB hack.

Richard don't get disheartened it will be something simple.

You need to break this down into small pieces.
First you need to verify the wiring is correct so check this first.
Then you need to detemine if the signals are getting through and the BOB Hack worked.

Now Mach3.!

Mach3 or any other controller for that matter all work the same in that they need to communicate with outside world through some external device, in your case the parallel port which is connected to the BOB you messed with. They do this by taking the PIN #'s which are connected to physical devices on the machine and assigning them to functions the controller deals with.

Now Mach3 can be broken down into 4 separate sections which control the working of the machine. INPUTS, OUTPUTS, MOTOR OUTPUTS and SPINDLE.
You are only interested in the INPUTS section because a LIMIT is telling mach3 to DO SOMETHING.

I'm going to give an example just setting up the X axis, just repeat for the other axis and change the PIn #.

So first you need to know which PIN # you connected the X axis Limit switch to. I'm going to use PIN 11 in this example.

So go to the PORTS N PINS / INPUTS section of mach3 and you'll see X++ and X-- enable these with green tick. Next is the port # this will usually be 1 if using parallel port.
Next is the PIN Number, in this example I'm entering 11.

Finally the Active Low.
This is toggled depending on how you wired the switch. ie: NO or NC
If you wired NC (normally closed) switches then you want Mach3 to DO SOMETHING when the switch goes LOW, or put another way when it sees the voltage on PIN11 switch OFF.
If you wired them NO (normally open) then mach would only DO SOMETHING when it sees voltage appear on the PIN. The PIN goes HIGH.

It's that simple and if your BOB is letting the Signals through and the wiring is correct then Mach3 will see them and respond.

HOWEVER if any of these settings is wrong then Mach3 knows nothing and will DO NOTHING. It's common with new users to Blame Mach3 but mach3 only does what YOU tell it so if you give it Duff Info or it doesn't see the Signals getting through then it won't work now matter how much they bitch about it.

If you are sure you have the correct PIN # entered and the Port # and it still doesn't work then it's 99% either the BOB or the Wiring not letting the signal through.